diff --git a/src/renderer/components/extensions/mcp/CustomMcpServerDialog.tsx b/src/renderer/components/extensions/mcp/CustomMcpServerDialog.tsx
index bba98439..66fc266d 100644
--- a/src/renderer/components/extensions/mcp/CustomMcpServerDialog.tsx
+++ b/src/renderer/components/extensions/mcp/CustomMcpServerDialog.tsx
@@ -3,7 +3,7 @@
  * Supports stdio (npm package) and HTTP/SSE transports.
  */
 
-import { useEffect, useState } from 'react';
+import { useEffect, useRef, useState } from 'react';
 
 import { api } from '@renderer/api';
 import { Button } from '@renderer/components/ui/button';
@@ -92,11 +92,15 @@ export const CustomMcpServerDialog = ({
   const [envVars, setEnvVars] = useState<EnvEntry[]>([]);
   const [error, setError] = useState<string | null>(null);
   const [installing, setInstalling] = useState(false);
+  const autoFilledValuesRef = useRef<Record<string, string>>({});
   const envVarLookupNames = envVars
     .map((entry) => entry.key.trim())
     .filter(Boolean)
     .sort()
     .join('\0');
+  const apiKeyLookupProjectPath = isProjectScopedMcpScope(scope)
+    ? (projectPath ?? undefined)
+    : undefined;
 
   // Reset on open
   useEffect(() => {
@@ -112,6 +116,7 @@ export const CustomMcpServerDialog = ({
       setEnvVars([]);
       setError(null);
       setInstalling(false);
+      autoFilledValuesRef.current = {};
     }
   }, [defaultSharedScope, open]);
 
@@ -128,19 +133,50 @@ export const CustomMcpServerDialog = ({
     const envVarNames = envVars.map((e) => e.key.trim()).filter(Boolean);
     if (envVarNames.length === 0) return;
 
-    void api.apiKeys.lookup(envVarNames, projectPath ?? undefined).then(
+    void api.apiKeys.lookup(envVarNames, apiKeyLookupProjectPath).then(
       (results) => {
-        if (results.length === 0) return;
-        const lookup = new Map(results.map((r) => [r.envVarName, r.value]));
-        setEnvVars((prev) =>
-          prev.map((e) => (lookup.has(e.key) && !e.value ? { ...e, value: lookup.get(e.key)! } : e))
+        const previousAutoFilledValues = autoFilledValuesRef.current;
+        const nextAutoFilledValues = Object.fromEntries(
+          results.map((result) => [result.envVarName, result.value])
         );
+        setEnvVars((prev) => {
+          let changed = false;
+          const next = prev.map((entry) => {
+            const envVarName = entry.key.trim();
+            if (!envVarName) {
+              return entry;
+            }
+
+            const previousValue = previousAutoFilledValues[envVarName];
+            const nextValue = nextAutoFilledValues[envVarName];
+
+            if (!nextValue) {
+              if (previousValue && entry.value === previousValue) {
+                changed = true;
+                return { ...entry, value: '' };
+              }
+              return entry;
+            }
+
+            if (!entry.value || entry.value === previousValue) {
+              if (entry.value !== nextValue) {
+                changed = true;
+                return { ...entry, value: nextValue };
+              }
+            }
+
+            return entry;
+          });
+
+          return changed ? next : prev;
+        });
+        autoFilledValuesRef.current = nextAutoFilledValues;
       },
       () => {
         // Silently fail
       }
     );
-  }, [envVarLookupNames, envVars, open, projectPath]); // eslint-disable-line react-hooks/exhaustive-deps
+  }, [apiKeyLookupProjectPath, envVarLookupNames, open]); // eslint-disable-line react-hooks/exhaustive-deps
 
   const handleInstall = async () => {
     setError(null);
diff --git a/src/renderer/components/extensions/mcp/McpServerDetailDialog.tsx b/src/renderer/components/extensions/mcp/McpServerDetailDialog.tsx
index 8ac44ee7..10fb5579 100644
--- a/src/renderer/components/extensions/mcp/McpServerDetailDialog.tsx
+++ b/src/renderer/components/extensions/mcp/McpServerDetailDialog.tsx
@@ -3,7 +3,7 @@
  * Uses Radix UI Kit for all form elements.
  */
 
-import { useEffect, useState } from 'react';
+import { useEffect, useRef, useState } from 'react';
 
 import { api } from '@renderer/api';
 import { Badge } from '@renderer/components/ui/badge';
@@ -92,6 +92,7 @@ export const McpServerDetailDialog = ({
   const [headers, setHeaders] = useState<McpHeaderDef[]>([]);
   const [imgError, setImgError] = useState(false);
   const [autoFilledFields, setAutoFilledFields] = useState<Set<string>>(new Set());
+  const autoFilledValuesRef = useRef<Record<string, string>>({});
   const normalizedInstalledEntries = installedEntries.length
     ? installedEntries
     : installedEntry
@@ -115,6 +116,9 @@ export const McpServerDetailDialog = ({
       .map((entry) => entry.name)
       .sort()
       .join('\0') ?? '';
+  const apiKeyLookupProjectPath = isProjectScopedMcpScope(scope)
+    ? (projectPath ?? undefined)
+    : undefined;
 
   // Initialize form when dialog opens or server changes
   useEffect(() => {
@@ -138,6 +142,7 @@ export const McpServerDetailDialog = ({
     setScope((preferredInstalledEntry?.scope as Scope | undefined) ?? defaultSharedScope);
     setImgError(false);
     setAutoFilledFields(new Set());
+    autoFilledValuesRef.current = {};
   }, [
     defaultSharedScope,
     open,
@@ -165,23 +170,38 @@ export const McpServerDetailDialog = ({
     if (!server || !open || server.envVars.length === 0 || !api.apiKeys) return;
 
     const envVarNames = server.envVars.map((e) => e.name);
-    void api.apiKeys.lookup(envVarNames, projectPath ?? undefined).then(
+    void api.apiKeys.lookup(envVarNames, apiKeyLookupProjectPath).then(
       (results) => {
-        if (results.length === 0) return;
-        const filled = new Set<string>();
-        const values: Record<string, string> = {};
+        const previousAutoFilledValues = autoFilledValuesRef.current;
+        const nextAutoFilledValues: Record<string, string> = {};
         for (const r of results) {
-          values[r.envVarName] = r.value;
-          filled.add(r.envVarName);
+          nextAutoFilledValues[r.envVarName] = r.value;
         }
-        setEnvValues((prev) => ({ ...prev, ...values }));
-        setAutoFilledFields(filled);
+        setEnvValues((prev) => {
+          const next = { ...prev };
+
+          for (const [envVarName, previousValue] of Object.entries(previousAutoFilledValues)) {
+            if (!(envVarName in nextAutoFilledValues) && next[envVarName] === previousValue) {
+              next[envVarName] = '';
+            }
+          }
+
+          for (const [envVarName, nextValue] of Object.entries(nextAutoFilledValues)) {
+            if (!next[envVarName] || next[envVarName] === previousAutoFilledValues[envVarName]) {
+              next[envVarName] = nextValue;
+            }
+          }
+
+          return next;
+        });
+        setAutoFilledFields(new Set(Object.keys(nextAutoFilledValues)));
+        autoFilledValuesRef.current = nextAutoFilledValues;
       },
       () => {
         // Silently fail — auto-fill is supplementary
       }
     );
-  }, [envVarLookupNames, open, projectPath, server?.id]); // eslint-disable-line react-hooks/exhaustive-deps
+  }, [apiKeyLookupProjectPath, envVarLookupNames, open, server?.id]); // eslint-disable-line react-hooks/exhaustive-deps
 
   if (!server) return <></>;
 
diff --git a/test/renderer/components/extensions/mcp/CustomMcpServerDialog.test.ts b/test/renderer/components/extensions/mcp/CustomMcpServerDialog.test.ts
index 29e23faa..177ffa11 100644
--- a/test/renderer/components/extensions/mcp/CustomMcpServerDialog.test.ts
+++ b/test/renderer/components/extensions/mcp/CustomMcpServerDialog.test.ts
@@ -180,7 +180,7 @@ describe('CustomMcpServerDialog project scope', () => {
     });
   });
 
-  it('passes projectPath into API key lookup for project-aware autofill', async () => {
+  it('looks up project-scoped API keys only when project scope is selected', async () => {
     const host = document.createElement('div');
     document.body.appendChild(host);
     const root = createRoot(host);
@@ -213,7 +213,88 @@ describe('CustomMcpServerDialog project scope', () => {
       await Promise.resolve();
     });
 
-    expect(lookupMock).toHaveBeenCalledWith(['CONTEXT7_API_KEY'], '/tmp/custom-mcp-project');
+    expect(lookupMock).toHaveBeenCalledWith(['CONTEXT7_API_KEY'], undefined);
+
+    const scopeSelect = host.querySelector('[data-testid="scope-select"]') as HTMLSelectElement;
+    await act(async () => {
+      setNativeValue(scopeSelect, 'project', 'change');
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(lookupMock).toHaveBeenLastCalledWith(['CONTEXT7_API_KEY'], '/tmp/custom-mcp-project');
+
+    await act(async () => {
+      setNativeValue(scopeSelect, 'user', 'change');
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(lookupMock).toHaveBeenLastCalledWith(['CONTEXT7_API_KEY'], undefined);
+
+    await act(async () => {
+      root.unmount();
+      await Promise.resolve();
+    });
+  });
+
+  it('clears stale project auto-filled values when switching back to user scope', async () => {
+    const host = document.createElement('div');
+    document.body.appendChild(host);
+    const root = createRoot(host);
+    lookupMock
+      .mockResolvedValueOnce([])
+      .mockResolvedValueOnce([{ envVarName: 'CONTEXT7_API_KEY', value: 'project-secret' }])
+      .mockResolvedValueOnce([]);
+
+    await act(async () => {
+      root.render(
+        React.createElement(CustomMcpServerDialog, {
+          open: true,
+          onClose: vi.fn(),
+          projectPath: '/tmp/custom-mcp-project',
+        })
+      );
+      await Promise.resolve();
+    });
+
+    const addEnvButton = Array.from(host.querySelectorAll('button')).find((button) =>
+      button.textContent?.includes('Add')
+    ) as HTMLButtonElement;
+    await act(async () => {
+      addEnvButton.click();
+      await Promise.resolve();
+    });
+
+    const envKeyInput = host.querySelector(
+      'input[placeholder="ENV_VAR_NAME"]'
+    ) as HTMLInputElement;
+    const envValueInput = host.querySelector(
+      'input[placeholder="value"]'
+    ) as HTMLInputElement;
+    const scopeSelect = host.querySelector('[data-testid="scope-select"]') as HTMLSelectElement;
+
+    await act(async () => {
+      setNativeValue(envKeyInput, 'CONTEXT7_API_KEY', 'input');
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    await act(async () => {
+      setNativeValue(scopeSelect, 'project', 'change');
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(envValueInput.value).toBe('project-secret');
+
+    await act(async () => {
+      setNativeValue(scopeSelect, 'user', 'change');
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(envValueInput.value).toBe('');
 
     await act(async () => {
       root.unmount();
diff --git a/test/renderer/components/extensions/mcp/McpServerDetailDialog.test.ts b/test/renderer/components/extensions/mcp/McpServerDetailDialog.test.ts
index 18c78c6d..14fe2b8c 100644
--- a/test/renderer/components/extensions/mcp/McpServerDetailDialog.test.ts
+++ b/test/renderer/components/extensions/mcp/McpServerDetailDialog.test.ts
@@ -278,7 +278,7 @@ describe('McpServerDetailDialog installed entry handling', () => {
     });
   });
 
-  it('passes projectPath into API key lookup for project-aware autofill', async () => {
+  it('looks up project-scoped API keys only when project scope is selected', async () => {
     const host = document.createElement('div');
     document.body.appendChild(host);
     const root = createRoot(host);
@@ -302,7 +302,81 @@ describe('McpServerDetailDialog installed entry handling', () => {
       await Promise.resolve();
     });
 
-    expect(lookupMock).toHaveBeenCalledWith(['CONTEXT7_API_KEY'], '/tmp/project-context7');
+    expect(lookupMock).toHaveBeenCalledWith(['CONTEXT7_API_KEY'], undefined);
+
+    const scopeSelect = host.querySelector('[data-testid="scope-select"]') as HTMLSelectElement;
+    await act(async () => {
+      scopeSelect.value = 'project';
+      scopeSelect.dispatchEvent(new Event('change', { bubbles: true }));
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(lookupMock).toHaveBeenLastCalledWith(['CONTEXT7_API_KEY'], '/tmp/project-context7');
+
+    await act(async () => {
+      scopeSelect.value = 'user';
+      scopeSelect.dispatchEvent(new Event('change', { bubbles: true }));
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(lookupMock).toHaveBeenLastCalledWith(['CONTEXT7_API_KEY'], undefined);
+
+    await act(async () => {
+      root.unmount();
+      await Promise.resolve();
+    });
+  });
+
+  it('clears stale project auto-filled values when switching back to user scope', async () => {
+    const host = document.createElement('div');
+    document.body.appendChild(host);
+    const root = createRoot(host);
+    const server = makeServer();
+    server.envVars = [{ name: 'CONTEXT7_API_KEY', isSecret: true }];
+    lookupMock
+      .mockResolvedValueOnce([])
+      .mockResolvedValueOnce([{ envVarName: 'CONTEXT7_API_KEY', value: 'project-secret' }])
+      .mockResolvedValueOnce([]);
+
+    await act(async () => {
+      root.render(
+        React.createElement(McpServerDetailDialog, {
+          server,
+          isInstalled: false,
+          installedEntry: null,
+          diagnostic: null,
+          diagnosticsLoading: false,
+          projectPath: '/tmp/project-context7',
+          open: true,
+          onClose: vi.fn(),
+        })
+      );
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    const scopeSelect = host.querySelector('[data-testid="scope-select"]') as HTMLSelectElement;
+    const envValueInput = host.querySelector('input[type="password"]') as HTMLInputElement;
+
+    await act(async () => {
+      scopeSelect.value = 'project';
+      scopeSelect.dispatchEvent(new Event('change', { bubbles: true }));
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(envValueInput.value).toBe('project-secret');
+
+    await act(async () => {
+      scopeSelect.value = 'user';
+      scopeSelect.dispatchEvent(new Event('change', { bubbles: true }));
+      await Promise.resolve();
+      await Promise.resolve();
+    });
+
+    expect(envValueInput.value).toBe('');
 
     await act(async () => {
       root.unmount();