diff --git a/app/src-tauri/Cargo.lock b/app/src-tauri/Cargo.lock
index c2bf53f..b74a626 100644
--- a/app/src-tauri/Cargo.lock
+++ b/app/src-tauri/Cargo.lock
@@ -404,6 +404,12 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
+[[package]]
+name = "byteorder-lite"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f1fe948ff07f4bd06c30984e69f5b4899c516a3ef74f34df92a2df2ab535495"
+
 [[package]]
 name = "bytes"
 version = "1.11.1"
@@ -1745,7 +1751,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3e795dff5605e0f04bff85ca41b51a96b83e80b281e96231bcaaf1ac35103371"
 dependencies = [
  "byteorder",
- "png",
+ "png 0.17.16",
 ]
 
 [[package]]
@@ -1862,6 +1868,19 @@ dependencies = [
  "icu_properties",
 ]
 
+[[package]]
+name = "image"
+version = "0.25.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6506c6c10786659413faa717ceebcb8f70731c0a60cbae39795fdf114519c1a"
+dependencies = [
+ "bytemuck",
+ "byteorder-lite",
+ "moxcms",
+ "num-traits",
+ "png 0.18.1",
+]
+
 [[package]]
 name = "indexmap"
 version = "1.9.3"
@@ -2265,6 +2284,16 @@ dependencies = [
  "windows-sys 0.61.2",
 ]
 
+[[package]]
+name = "moxcms"
+version = "0.7.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac9557c559cd6fc9867e122e20d2cbefc9ca29d80d027a8e39310920ed2f0a97"
+dependencies = [
+ "num-traits",
+ "pxfm",
+]
+
 [[package]]
 name = "muda"
 version = "0.17.1"
@@ -2280,7 +2309,7 @@ dependencies = [
  "objc2-core-foundation",
  "objc2-foundation",
  "once_cell",
- "png",
+ "png 0.17.16",
  "serde",
  "thiserror 2.0.18",
  "windows-sys 0.60.2",
@@ -2872,6 +2901,19 @@ dependencies = [
  "miniz_oxide",
 ]
 
+[[package]]
+name = "png"
+version = "0.18.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "60769b8b31b2a9f263dae2776c37b1b28ae246943cf719eb6946a1db05128a61"
+dependencies = [
+ "bitflags 2.11.0",
+ "crc32fast",
+ "fdeflate",
+ "flate2",
+ "miniz_oxide",
+]
+
 [[package]]
 name = "polling"
 version = "3.11.0"
@@ -3009,6 +3051,15 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "pxfm"
+version = "0.1.27"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7186d3822593aa4393561d186d1393b3923e9d6163d3fbfd6e825e3e6cf3e6a8"
+dependencies = [
+ "num-traits",
+]
+
 [[package]]
 name = "quick-xml"
 version = "0.38.4"
@@ -4076,6 +4127,7 @@ dependencies = [
  "gtk",
  "heck 0.5.0",
  "http",
+ "image",
  "jni",
  "libc",
  "log",
@@ -4143,7 +4195,7 @@ dependencies = [
  "ico",
  "json-patch",
  "plist",
- "png",
+ "png 0.17.16",
  "proc-macro2",
  "quote",
  "semver",
@@ -4728,7 +4780,7 @@ dependencies = [
  "objc2-core-graphics",
  "objc2-foundation",
  "once_cell",
- "png",
+ "png 0.17.16",
  "serde",
  "thiserror 2.0.18",
  "windows-sys 0.60.2",
diff --git a/app/src-tauri/src/commands/project_commands.rs b/app/src-tauri/src/commands/project_commands.rs
index 6da0e21..006a1ed 100644
--- a/app/src-tauri/src/commands/project_commands.rs
+++ b/app/src-tauri/src/commands/project_commands.rs
@@ -170,6 +170,7 @@ pub async fn start_project_container(
                     &existing_id,
                     &project,
                     settings.global_claude_instructions.as_deref(),
+                    &settings.global_custom_env_vars,
                 )
                 .await
                 .unwrap_or(false);
@@ -185,6 +186,7 @@ pub async fn start_project_container(
                     aws_config_path.as_deref(),
                     &settings.global_aws,
                     settings.global_claude_instructions.as_deref(),
+                    &settings.global_custom_env_vars,
                 ).await?;
                 docker::start_container(&new_id).await?;
                 new_id
@@ -201,6 +203,7 @@ pub async fn start_project_container(
                 aws_config_path.as_deref(),
                 &settings.global_aws,
                 settings.global_claude_instructions.as_deref(),
+                &settings.global_custom_env_vars,
             ).await?;
             docker::start_container(&new_id).await?;
             new_id
diff --git a/app/src-tauri/src/docker/container.rs b/app/src-tauri/src/docker/container.rs
index 27955ff..c4264ef 100644
--- a/app/src-tauri/src/docker/container.rs
+++ b/app/src-tauri/src/docker/container.rs
@@ -30,6 +30,25 @@ fn compute_env_fingerprint(custom_env_vars: &[EnvVar]) -> String {
     parts.join(",")
 }
 
+/// Merge global and per-project custom environment variables.
+/// Per-project variables override global variables with the same key.
+fn merge_custom_env_vars(global: &[EnvVar], project: &[EnvVar]) -> Vec<EnvVar> {
+    let mut merged: std::collections::HashMap<String, EnvVar> = std::collections::HashMap::new();
+    for ev in global {
+        let key = ev.key.trim().to_string();
+        if !key.is_empty() {
+            merged.insert(key, ev.clone());
+        }
+    }
+    for ev in project {
+        let key = ev.key.trim().to_string();
+        if !key.is_empty() {
+            merged.insert(key, ev.clone());
+        }
+    }
+    merged.into_values().collect()
+}
+
 /// Merge global and per-project Claude instructions into a single string.
 fn merge_claude_instructions(
     global_instructions: Option<&str>,
@@ -114,6 +133,7 @@ pub async fn create_container(
     aws_config_path: Option<&str>,
     global_aws: &GlobalAwsSettings,
     global_claude_instructions: Option<&str>,
+    global_custom_env_vars: &[EnvVar],
 ) -> Result<String, String> {
     let docker = get_docker()?;
     let container_name = project.container_name();
@@ -222,9 +242,10 @@ pub async fn create_container(
         }
     }
 
-    // Custom environment variables
+    // Custom environment variables (global + per-project, project overrides global for same key)
+    let merged_env = merge_custom_env_vars(global_custom_env_vars, &project.custom_env_vars);
     let reserved_prefixes = ["ANTHROPIC_", "AWS_", "GIT_", "HOST_", "CLAUDE_", "TRIPLE_C_"];
-    for env_var in &project.custom_env_vars {
+    for env_var in &merged_env {
         let key = env_var.key.trim();
         if key.is_empty() {
             continue;
@@ -236,7 +257,7 @@ pub async fn create_container(
         }
         env_vars.push(format!("{}={}", key, env_var.value));
     }
-    let custom_env_fingerprint = compute_env_fingerprint(&project.custom_env_vars);
+    let custom_env_fingerprint = compute_env_fingerprint(&merged_env);
     env_vars.push(format!("TRIPLE_C_CUSTOM_ENV={}", custom_env_fingerprint));
 
     // Claude instructions (global + per-project)
@@ -419,6 +440,7 @@ pub async fn container_needs_recreation(
     container_id: &str,
     project: &Project,
     global_claude_instructions: Option<&str>,
+    global_custom_env_vars: &[EnvVar],
 ) -> Result<bool, String> {
     let docker = get_docker()?;
     let info = docker
@@ -547,7 +569,8 @@ pub async fn container_needs_recreation(
     }
 
     // ── Custom environment variables ──────────────────────────────────────
-    let expected_fingerprint = compute_env_fingerprint(&project.custom_env_vars);
+    let merged_env = merge_custom_env_vars(global_custom_env_vars, &project.custom_env_vars);
+    let expected_fingerprint = compute_env_fingerprint(&merged_env);
     let container_fingerprint = get_env("TRIPLE_C_CUSTOM_ENV").unwrap_or_default();
     if container_fingerprint != expected_fingerprint {
         log::info!("Custom env vars mismatch (container={:?}, expected={:?})", container_fingerprint, expected_fingerprint);
diff --git a/app/src-tauri/src/lib.rs b/app/src-tauri/src/lib.rs
index c01435c..80bdcab 100644
--- a/app/src-tauri/src/lib.rs
+++ b/app/src-tauri/src/lib.rs
@@ -27,7 +27,7 @@ pub fn run() {
             exec_manager: ExecSessionManager::new(),
         })
         .setup(|app| {
-            let icon = tauri::image::Image::from_bytes(include_bytes!("../icons/icon.png"))
+            let icon = tauri::image::Image::from_bytes(include_bytes!("../icons/icon.ico"))
                 .expect("Failed to load window icon");
             if let Some(window) = app.get_webview_window("main") {
                 let _ = window.set_icon(icon);
diff --git a/app/src-tauri/src/models/app_settings.rs b/app/src-tauri/src/models/app_settings.rs
index 79ab006..ddc1e81 100644
--- a/app/src-tauri/src/models/app_settings.rs
+++ b/app/src-tauri/src/models/app_settings.rs
@@ -1,9 +1,15 @@
 use serde::{Deserialize, Serialize};
 
+use super::project::EnvVar;
+
 fn default_true() -> bool {
     true
 }
 
+fn default_global_instructions() -> Option<String> {
+    Some("If the project is not initialized with git, recommend to the user to initialize and use git to track changes. This makes it easier to revert should something break.".to_string())
+}
+
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
 #[serde(rename_all = "snake_case")]
 pub enum ImageSource {
@@ -54,8 +60,10 @@ pub struct AppSettings {
     pub custom_image_name: Option<String>,
     #[serde(default)]
     pub global_aws: GlobalAwsSettings,
-    #[serde(default)]
+    #[serde(default = "default_global_instructions")]
     pub global_claude_instructions: Option<String>,
+    #[serde(default)]
+    pub global_custom_env_vars: Vec<EnvVar>,
     #[serde(default = "default_true")]
     pub auto_check_updates: bool,
     #[serde(default)]
@@ -72,7 +80,8 @@ impl Default for AppSettings {
             image_source: ImageSource::default(),
             custom_image_name: None,
             global_aws: GlobalAwsSettings::default(),
-            global_claude_instructions: None,
+            global_claude_instructions: default_global_instructions(),
+            global_custom_env_vars: Vec::new(),
             auto_check_updates: true,
             dismissed_update_version: None,
         }
diff --git a/app/src/components/projects/ClaudeInstructionsModal.tsx b/app/src/components/projects/ClaudeInstructionsModal.tsx
new file mode 100644
index 0000000..7c1c516
--- /dev/null
+++ b/app/src/components/projects/ClaudeInstructionsModal.tsx
@@ -0,0 +1,80 @@
+import { useState, useEffect, useRef, useCallback } from "react";
+
+interface Props {
+  instructions: string;
+  disabled: boolean;
+  onSave: (instructions: string) => Promise<void>;
+  onClose: () => void;
+}
+
+export default function ClaudeInstructionsModal({ instructions: initial, disabled, onSave, onClose }: Props) {
+  const [instructions, setInstructions] = useState(initial);
+  const overlayRef = useRef<HTMLDivElement>(null);
+  const textareaRef = useRef<HTMLTextAreaElement>(null);
+
+  useEffect(() => {
+    textareaRef.current?.focus();
+  }, []);
+
+  useEffect(() => {
+    const handleKeyDown = (e: KeyboardEvent) => {
+      if (e.key === "Escape") onClose();
+    };
+    document.addEventListener("keydown", handleKeyDown);
+    return () => document.removeEventListener("keydown", handleKeyDown);
+  }, [onClose]);
+
+  const handleOverlayClick = useCallback(
+    (e: React.MouseEvent<HTMLDivElement>) => {
+      if (e.target === overlayRef.current) onClose();
+    },
+    [onClose],
+  );
+
+  const handleBlur = async () => {
+    try { await onSave(instructions); } catch (err) {
+      console.error("Failed to update Claude instructions:", err);
+    }
+  };
+
+  return (
+    <div
+      ref={overlayRef}
+      onClick={handleOverlayClick}
+      className="fixed inset-0 bg-black/50 flex items-center justify-center z-50"
+    >
+      <div className="bg-[var(--bg-secondary)] border border-[var(--border-color)] rounded-lg p-6 w-[40rem] shadow-xl max-h-[80vh] flex flex-col">
+        <h2 className="text-lg font-semibold mb-1">Claude Instructions</h2>
+        <p className="text-xs text-[var(--text-secondary)] mb-4">
+          Per-project instructions for Claude Code (written to ~/.claude/CLAUDE.md in container)
+        </p>
+
+        {disabled && (
+          <div className="px-2 py-1.5 mb-3 bg-[var(--warning)]/15 border border-[var(--warning)]/30 rounded text-xs text-[var(--warning)]">
+            Container must be stopped to change Claude instructions.
+          </div>
+        )}
+
+        <textarea
+          ref={textareaRef}
+          value={instructions}
+          onChange={(e) => setInstructions(e.target.value)}
+          onBlur={handleBlur}
+          placeholder="Enter instructions for Claude Code in this project's container..."
+          disabled={disabled}
+          rows={14}
+          className="w-full flex-1 px-3 py-2 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-sm text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 resize-y font-mono"
+        />
+
+        <div className="flex justify-end mt-4">
+          <button
+            onClick={onClose}
+            className="px-4 py-2 text-sm text-[var(--text-secondary)] hover:text-[var(--text-primary)] transition-colors"
+          >
+            Close
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+}
diff --git a/app/src/components/projects/EnvVarsModal.tsx b/app/src/components/projects/EnvVarsModal.tsx
new file mode 100644
index 0000000..f85ca75
--- /dev/null
+++ b/app/src/components/projects/EnvVarsModal.tsx
@@ -0,0 +1,124 @@
+import { useState, useEffect, useRef, useCallback } from "react";
+import type { EnvVar } from "../../lib/types";
+
+interface Props {
+  envVars: EnvVar[];
+  disabled: boolean;
+  onSave: (vars: EnvVar[]) => Promise<void>;
+  onClose: () => void;
+}
+
+export default function EnvVarsModal({ envVars: initial, disabled, onSave, onClose }: Props) {
+  const [vars, setVars] = useState<EnvVar[]>(initial);
+  const overlayRef = useRef<HTMLDivElement>(null);
+
+  useEffect(() => {
+    const handleKeyDown = (e: KeyboardEvent) => {
+      if (e.key === "Escape") onClose();
+    };
+    document.addEventListener("keydown", handleKeyDown);
+    return () => document.removeEventListener("keydown", handleKeyDown);
+  }, [onClose]);
+
+  const handleOverlayClick = useCallback(
+    (e: React.MouseEvent<HTMLDivElement>) => {
+      if (e.target === overlayRef.current) onClose();
+    },
+    [onClose],
+  );
+
+  const updateVar = (index: number, field: keyof EnvVar, value: string) => {
+    const updated = [...vars];
+    updated[index] = { ...updated[index], [field]: value };
+    setVars(updated);
+  };
+
+  const removeVar = async (index: number) => {
+    const updated = vars.filter((_, i) => i !== index);
+    setVars(updated);
+    try { await onSave(updated); } catch (err) {
+      console.error("Failed to remove environment variable:", err);
+    }
+  };
+
+  const addVar = async () => {
+    const updated = [...vars, { key: "", value: "" }];
+    setVars(updated);
+    try { await onSave(updated); } catch (err) {
+      console.error("Failed to add environment variable:", err);
+    }
+  };
+
+  const handleBlur = async () => {
+    try { await onSave(vars); } catch (err) {
+      console.error("Failed to update environment variables:", err);
+    }
+  };
+
+  return (
+    <div
+      ref={overlayRef}
+      onClick={handleOverlayClick}
+      className="fixed inset-0 bg-black/50 flex items-center justify-center z-50"
+    >
+      <div className="bg-[var(--bg-secondary)] border border-[var(--border-color)] rounded-lg p-6 w-[36rem] shadow-xl max-h-[80vh] overflow-y-auto">
+        <h2 className="text-lg font-semibold mb-4">Environment Variables</h2>
+
+        {disabled && (
+          <div className="px-2 py-1.5 mb-3 bg-[var(--warning)]/15 border border-[var(--warning)]/30 rounded text-xs text-[var(--warning)]">
+            Container must be stopped to change environment variables.
+          </div>
+        )}
+
+        <div className="space-y-2 mb-4">
+          {vars.length === 0 && (
+            <p className="text-xs text-[var(--text-secondary)]">No environment variables configured.</p>
+          )}
+          {vars.map((ev, i) => (
+            <div key={i} className="flex gap-2 items-center">
+              <input
+                value={ev.key}
+                onChange={(e) => updateVar(i, "key", e.target.value)}
+                onBlur={handleBlur}
+                placeholder="KEY"
+                disabled={disabled}
+                className="w-2/5 px-2 py-1.5 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-sm text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 font-mono"
+              />
+              <input
+                value={ev.value}
+                onChange={(e) => updateVar(i, "value", e.target.value)}
+                onBlur={handleBlur}
+                placeholder="value"
+                disabled={disabled}
+                className="flex-1 px-2 py-1.5 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-sm text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 font-mono"
+              />
+              <button
+                onClick={() => removeVar(i)}
+                disabled={disabled}
+                className="px-2 py-1.5 text-sm text-[var(--error)] hover:bg-[var(--bg-primary)] rounded disabled:opacity-50 transition-colors"
+              >
+                x
+              </button>
+            </div>
+          ))}
+        </div>
+
+        <div className="flex justify-between items-center">
+          <button
+            onClick={addVar}
+            disabled={disabled}
+            className="text-sm text-[var(--accent)] hover:text-[var(--accent-hover)] disabled:opacity-50 transition-colors"
+          >
+            + Add variable
+          </button>
+          <button
+            onClick={onClose}
+            className="px-4 py-2 text-sm text-[var(--text-secondary)] hover:text-[var(--text-primary)] transition-colors"
+          >
+            Close
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+}
diff --git a/app/src/components/projects/ProjectCard.tsx b/app/src/components/projects/ProjectCard.tsx
index 9cceae2..49db203 100644
--- a/app/src/components/projects/ProjectCard.tsx
+++ b/app/src/components/projects/ProjectCard.tsx
@@ -4,6 +4,8 @@ import type { Project, ProjectPath, AuthMode, BedrockConfig, BedrockAuthMethod }
 import { useProjects } from "../../hooks/useProjects";
 import { useTerminal } from "../../hooks/useTerminal";
 import { useAppState } from "../../store/appState";
+import EnvVarsModal from "./EnvVarsModal";
+import ClaudeInstructionsModal from "./ClaudeInstructionsModal";
 
 interface Props {
   project: Project;
@@ -17,6 +19,8 @@ export default function ProjectCard({ project }: Props) {
   const [loading, setLoading] = useState(false);
   const [error, setError] = useState<string | null>(null);
   const [showConfig, setShowConfig] = useState(false);
+  const [showEnvVarsModal, setShowEnvVarsModal] = useState(false);
+  const [showClaudeInstructionsModal, setShowClaudeInstructionsModal] = useState(false);
   const isSelected = selectedProjectId === project.id;
   const isStopped = project.status === "stopped" || project.status === "error";
 
@@ -165,22 +169,6 @@ export default function ProjectCard({ project }: Props) {
     }
   };
 
-  const handleClaudeInstructionsBlur = async () => {
-    try {
-      await update({ ...project, claude_instructions: claudeInstructions || null });
-    } catch (err) {
-      console.error("Failed to update Claude instructions:", err);
-    }
-  };
-
-  const handleEnvVarBlur = async () => {
-    try {
-      await update({ ...project, custom_env_vars: envVars });
-    } catch (err) {
-      console.error("Failed to update environment variables:", err);
-    }
-  };
-
   const handleBedrockRegionBlur = async () => {
     try {
       const current = project.bedrock_config ?? defaultBedrockConfig;
@@ -358,6 +346,11 @@ export default function ProjectCard({ project }: Props) {
           {/* Config panel */}
           {showConfig && (
             <div className="space-y-2 pt-1 border-t border-[var(--border-color)] min-w-0 overflow-hidden" onClick={(e) => e.stopPropagation()}>
+              {!isStopped && (
+                <div className="px-2 py-1.5 bg-[var(--warning)]/15 border border-[var(--warning)]/30 rounded text-xs text-[var(--warning)]">
+                  Container must be stopped to change settings.
+                </div>
+              )}
               {/* Folder paths */}
               <div>
                 <label className="block text-xs text-[var(--text-secondary)] mb-0.5">Folders</label>
@@ -530,76 +523,29 @@ export default function ProjectCard({ project }: Props) {
               </div>
 
               {/* Environment Variables */}
-              <div>
-                <label className="block text-xs text-[var(--text-secondary)] mb-0.5">Environment Variables</label>
-                {envVars.map((ev, i) => (
-                  <div key={i} className="flex gap-1 mb-1">
-                    <input
-                      value={ev.key}
-                      onChange={(e) => {
-                        const vars = [...envVars];
-                        vars[i] = { ...vars[i], key: e.target.value };
-                        setEnvVars(vars);
-                      }}
-                      onBlur={handleEnvVarBlur}
-                      placeholder="KEY"
-                      disabled={!isStopped}
-                      className="w-1/3 px-2 py-1 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-xs text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 font-mono"
-                    />
-                    <input
-                      value={ev.value}
-                      onChange={(e) => {
-                        const vars = [...envVars];
-                        vars[i] = { ...vars[i], value: e.target.value };
-                        setEnvVars(vars);
-                      }}
-                      onBlur={handleEnvVarBlur}
-                      placeholder="value"
-                      disabled={!isStopped}
-                      className="flex-1 px-2 py-1 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-xs text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 font-mono"
-                    />
-                    <button
-                      onClick={async () => {
-                        const vars = envVars.filter((_, j) => j !== i);
-                        setEnvVars(vars);
-                        try { await update({ ...project, custom_env_vars: vars }); } catch (err) {
-                          console.error("Failed to remove environment variable:", err);
-                        }
-                      }}
-                      disabled={!isStopped}
-                      className="px-1.5 py-1 text-xs text-[var(--error)] hover:bg-[var(--bg-primary)] rounded disabled:opacity-50 transition-colors"
-                    >
-                      x
-                    </button>
-                  </div>
-                ))}
+              <div className="flex items-center justify-between">
+                <label className="text-xs text-[var(--text-secondary)]">
+                  Environment Variables{envVars.length > 0 && ` (${envVars.length})`}
+                </label>
                 <button
-                  onClick={async () => {
-                    const vars = [...envVars, { key: "", value: "" }];
-                    setEnvVars(vars);
-                    try { await update({ ...project, custom_env_vars: vars }); } catch (err) {
-                      console.error("Failed to add environment variable:", err);
-                    }
-                  }}
-                  disabled={!isStopped}
-                  className="text-xs text-[var(--accent)] hover:text-[var(--accent-hover)] disabled:opacity-50 transition-colors"
+                  onClick={() => setShowEnvVarsModal(true)}
+                  className="text-xs px-2 py-0.5 text-[var(--accent)] hover:text-[var(--accent-hover)] hover:bg-[var(--bg-primary)] rounded transition-colors"
                 >
-                  + Add variable
+                  Edit
                 </button>
               </div>
 
               {/* Claude Instructions */}
-              <div>
-                <label className="block text-xs text-[var(--text-secondary)] mb-0.5">Claude Instructions</label>
-                <textarea
-                  value={claudeInstructions}
-                  onChange={(e) => setClaudeInstructions(e.target.value)}
-                  onBlur={handleClaudeInstructionsBlur}
-                  placeholder="Per-project instructions for Claude Code (written to ~/.claude/CLAUDE.md in container)"
-                  disabled={!isStopped}
-                  rows={3}
-                  className="w-full px-2 py-1 bg-[var(--bg-primary)] border border-[var(--border-color)] rounded text-xs text-[var(--text-primary)] focus:outline-none focus:border-[var(--accent)] disabled:opacity-50 resize-y font-mono"
-                />
+              <div className="flex items-center justify-between">
+                <label className="text-xs text-[var(--text-secondary)]">
+                  Claude Instructions{claudeInstructions ? " (set)" : ""}
+                </label>
+                <button
+                  onClick={() => setShowClaudeInstructionsModal(true)}
+                  className="text-xs px-2 py-0.5 text-[var(--accent)] hover:text-[var(--accent-hover)] hover:bg-[var(--bg-primary)] rounded transition-colors"
+                >
+                  Edit
+                </button>
               </div>
 
               {/* Bedrock config */}
@@ -734,6 +680,30 @@ export default function ProjectCard({ project }: Props) {
       {error && (
         <div className="text-xs text-[var(--error)] mt-1 ml-4">{error}</div>
       )}
+
+      {showEnvVarsModal && (
+        <EnvVarsModal
+          envVars={envVars}
+          disabled={!isStopped}
+          onSave={async (vars) => {
+            setEnvVars(vars);
+            await update({ ...project, custom_env_vars: vars });
+          }}
+          onClose={() => setShowEnvVarsModal(false)}
+        />
+      )}
+
+      {showClaudeInstructionsModal && (
+        <ClaudeInstructionsModal
+          instructions={claudeInstructions}
+          disabled={!isStopped}
+          onSave={async (instructions) => {
+            setClaudeInstructions(instructions);
+            await update({ ...project, claude_instructions: instructions || null });
+          }}
+          onClose={() => setShowClaudeInstructionsModal(false)}
+        />
+      )}
     </div>
   );
 }
diff --git a/app/src/components/settings/SettingsPanel.tsx b/app/src/components/settings/SettingsPanel.tsx
index 698c744..f811423 100644
--- a/app/src/components/settings/SettingsPanel.tsx
+++ b/app/src/components/settings/SettingsPanel.tsx
@@ -4,22 +4,24 @@ import DockerSettings from "./DockerSettings";
 import AwsSettings from "./AwsSettings";
 import { useSettings } from "../../hooks/useSettings";
 import { useUpdates } from "../../hooks/useUpdates";
+import ClaudeInstructionsModal from "../projects/ClaudeInstructionsModal";
+import EnvVarsModal from "../projects/EnvVarsModal";
+import type { EnvVar } from "../../lib/types";
 
 export default function SettingsPanel() {
   const { appSettings, saveSettings } = useSettings();
   const { appVersion, checkForUpdates } = useUpdates();
   const [globalInstructions, setGlobalInstructions] = useState(appSettings?.global_claude_instructions ?? "");
+  const [globalEnvVars, setGlobalEnvVars] = useState<EnvVar[]>(appSettings?.global_custom_env_vars ?? []);
   const [checkingUpdates, setCheckingUpdates] = useState(false);
+  const [showInstructionsModal, setShowInstructionsModal] = useState(false);
+  const [showEnvVarsModal, setShowEnvVarsModal] = useState(false);
 
   // Sync local state when appSettings change
   useEffect(() => {
     setGlobalInstructions(appSettings?.global_claude_instructions ?? "");
-  }, [appSettings?.global_claude_instructions]);
-
-  const handleInstructionsBlur = async () => {
-    if (!appSettings) return;
-    await saveSettings({ ...appSettings, global_claude_instructions: globalInstructions || null });
-  };
+    setGlobalEnvVars(appSettings?.global_custom_env_vars ?? []);
+  }, [appSettings?.global_claude_instructions, appSettings?.global_custom_env_vars]);
 
   const handleCheckNow = async () => {
     setCheckingUpdates(true);
@@ -43,19 +45,43 @@ export default function SettingsPanel() {
       <ApiKeyInput />
       <DockerSettings />
       <AwsSettings />
+
+      {/* Global Claude Instructions */}
       <div>
-        <label className="block text-sm font-medium mb-2">Claude Instructions</label>
+        <label className="block text-sm font-medium mb-1">Claude Instructions</label>
         <p className="text-xs text-[var(--text-secondary)] mb-1.5">
           Global instructions applied to all projects (written to ~/.claude/CLAUDE.md in containers)
         </p>
-        <textarea
-          value={globalInstructions}
-          onChange={(e) => setGlobalInstructions(e.target.value)}
-          onBlur={handleInstructionsBlur}
-          placeholder="Instructions for Claude Code in all project containers..."
-          rows={4}
-          className="w-full px-2 py-1.5 text-xs bg-[var(--bg-primary)] border border-[var(--border-color)] rounded focus:outline-none focus:border-[var(--accent)] resize-y font-mono"
-        />
+        <div className="flex items-center justify-between">
+          <span className="text-xs text-[var(--text-secondary)]">
+            {globalInstructions ? "Configured" : "Not set"}
+          </span>
+          <button
+            onClick={() => setShowInstructionsModal(true)}
+            className="text-xs px-2 py-0.5 text-[var(--accent)] hover:text-[var(--accent-hover)] hover:bg-[var(--bg-primary)] rounded transition-colors"
+          >
+            Edit
+          </button>
+        </div>
+      </div>
+
+      {/* Global Environment Variables */}
+      <div>
+        <label className="block text-sm font-medium mb-1">Global Environment Variables</label>
+        <p className="text-xs text-[var(--text-secondary)] mb-1.5">
+          Applied to all project containers. Per-project variables override global ones with the same key.
+        </p>
+        <div className="flex items-center justify-between">
+          <span className="text-xs text-[var(--text-secondary)]">
+            {globalEnvVars.length > 0 ? `${globalEnvVars.length} variable${globalEnvVars.length === 1 ? "" : "s"}` : "None"}
+          </span>
+          <button
+            onClick={() => setShowEnvVarsModal(true)}
+            className="text-xs px-2 py-0.5 text-[var(--accent)] hover:text-[var(--accent-hover)] hover:bg-[var(--bg-primary)] rounded transition-colors"
+          >
+            Edit
+          </button>
+        </div>
       </div>
 
       {/* Updates section */}
@@ -89,6 +115,34 @@ export default function SettingsPanel() {
           </button>
         </div>
       </div>
+
+      {showInstructionsModal && (
+        <ClaudeInstructionsModal
+          instructions={globalInstructions}
+          disabled={false}
+          onSave={async (instructions) => {
+            setGlobalInstructions(instructions);
+            if (appSettings) {
+              await saveSettings({ ...appSettings, global_claude_instructions: instructions || null });
+            }
+          }}
+          onClose={() => setShowInstructionsModal(false)}
+        />
+      )}
+
+      {showEnvVarsModal && (
+        <EnvVarsModal
+          envVars={globalEnvVars}
+          disabled={false}
+          onSave={async (vars) => {
+            setGlobalEnvVars(vars);
+            if (appSettings) {
+              await saveSettings({ ...appSettings, global_custom_env_vars: vars });
+            }
+          }}
+          onClose={() => setShowEnvVarsModal(false)}
+        />
+      )}
     </div>
   );
 }
diff --git a/app/src/lib/types.ts b/app/src/lib/types.ts
index 313408a..b616e86 100644
--- a/app/src/lib/types.ts
+++ b/app/src/lib/types.ts
@@ -88,6 +88,7 @@ export interface AppSettings {
   custom_image_name: string | null;
   global_aws: GlobalAwsSettings;
   global_claude_instructions: string | null;
+  global_custom_env_vars: EnvVar[];
   auto_check_updates: boolean;
   dismissed_update_version: string | null;
 }