diff --git a/packages/core/src/config/config.test.ts b/packages/core/src/config/config.test.ts
index da30b133775..d01b3448070 100644
--- a/packages/core/src/config/config.test.ts
+++ b/packages/core/src/config/config.test.ts
@@ -3116,3 +3116,23 @@ describe('Model Persistence Bug Fix (#19864)', () => {
     expect(config.getModel()).toBe(PREVIEW_GEMINI_3_1_MODEL);
   });
 });
+
+describe('isPathAllowed', () => {
+  it('should preserve casing when validating paths', () => {
+    const params: ConfigParameters = {
+      cwd: '/tmp',
+      targetDir: '/tmp/target',
+      model: DEFAULT_GEMINI_MODEL,
+      sessionId: 'test-session',
+      debugMode: false,
+    };
+    const config = new Config(params);
+    const workspaceContext = config.getWorkspaceContext();
+    const spy = vi.spyOn(workspaceContext, 'isPathWithinWorkspace');
+
+    const mixedCasePath = path.join('/tmp/target', 'SubDir', 'File.txt');
+    config.isPathAllowed(mixedCasePath);
+    expect(spy).toHaveBeenCalledWith(expect.stringMatching(/File\.txt$/));
+    expect(spy).toHaveBeenCalledWith(mixedCasePath);
+  });
+});
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index e4c0fef6ebd..7cb5e1411be 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -6,7 +6,6 @@
 
 import * as fs from 'node:fs';
 import * as path from 'node:path';
-import * as os from 'node:os';
 import { inspect } from 'node:util';
 import process from 'node:process';
 import {
@@ -2381,7 +2380,7 @@ export class Config implements McpContext {
       } catch {
         resolved = path.resolve(p);
       }
-      return os.platform() === 'win32' ? resolved.toLowerCase() : resolved;
+      return resolved;
     };
 
     const resolvedPath = realpath(absolutePath);
diff --git a/packages/core/src/config/projectRegistry.test.ts b/packages/core/src/config/projectRegistry.test.ts
index a441de8b3e2..846207a862b 100644
--- a/packages/core/src/config/projectRegistry.test.ts
+++ b/packages/core/src/config/projectRegistry.test.ts
@@ -107,6 +107,25 @@ describe('ProjectRegistry', () => {
     expect(id1).toBe(id2);
   });
 
+  it('preserves path casing on Windows', async () => {
+    // Regression test: Mixed-case paths MUST be preserved in the registry (not lowercased).
+    const registry = new ProjectRegistry(registryPath);
+    await registry.initialize();
+
+    const mixedCasePath = path.join(tempDir, 'MyProject');
+    const id = await registry.getShortId(mixedCasePath);
+
+    // IDs are slugified (lowercase), but path keys in registry must remain case-sensitive.
+    expect(id).toBe('myproject');
+
+    // Verify raw registry file data preserves path casing
+    const data = JSON.parse(fs.readFileSync(registryPath, 'utf8'));
+    const expectedKey = path.resolve(mixedCasePath);
+
+    expect(Object.keys(data.projects)).toContain(expectedKey);
+    expect(data.projects[expectedKey]).toBe('myproject');
+  });
+
   it('creates ownership markers in base directories', async () => {
     const registry = new ProjectRegistry(registryPath, [baseDir1, baseDir2]);
     await registry.initialize();
diff --git a/packages/core/src/config/projectRegistry.ts b/packages/core/src/config/projectRegistry.ts
index 725ea081f94..14b78cd97b3 100644
--- a/packages/core/src/config/projectRegistry.ts
+++ b/packages/core/src/config/projectRegistry.ts
@@ -6,7 +6,6 @@
 
 import * as fs from 'node:fs';
 import * as path from 'node:path';
-import * as os from 'node:os';
 import { lock } from 'proper-lockfile';
 import { debugLogger } from '../utils/debugLogger.js';
 
@@ -69,11 +68,7 @@ export class ProjectRegistry {
   }
 
   private normalizePath(projectPath: string): string {
-    let resolved = path.resolve(projectPath);
-    if (os.platform() === 'win32') {
-      resolved = resolved.toLowerCase();
-    }
-    return resolved;
+    return path.resolve(projectPath);
   }
 
   private async save(data: RegistryData): Promise<void> {
diff --git a/packages/core/src/utils/workspaceContext.test.ts b/packages/core/src/utils/workspaceContext.test.ts
index 8c29819a79e..c8c7a36cb43 100644
--- a/packages/core/src/utils/workspaceContext.test.ts
+++ b/packages/core/src/utils/workspaceContext.test.ts
@@ -139,6 +139,48 @@ describe('WorkspaceContext with real filesystem', () => {
       expect(workspaceContext.isPathWithinWorkspace(invalidPath)).toBe(false);
     });
 
+    it('should match paths case-insensitively on Windows', () => {
+      // Force win32 platform for this test
+      const originalPlatform = os.platform();
+      Object.defineProperty(process, 'platform', { value: 'win32' });
+
+      try {
+        // Setup: cwd is lowercase-ish, checkPath is MixedCase
+        // In the real fix, we normalize BOTH to lowercase for comparison.
+        // Let's assume cwd is '/tmp/project'
+        const lowerCwd = cwd.toLowerCase();
+        // Ensure the directory exists for the test to pass validation
+        if (!fs.existsSync(lowerCwd)) {
+          fs.mkdirSync(lowerCwd, { recursive: true });
+        }
+        const workspaceContext = new WorkspaceContext(lowerCwd);
+
+        // A path that matches case-insensitively
+        const mixedCasePath = path.join(lowerCwd, 'SubDir', 'File.txt');
+        expect(workspaceContext.isPathWithinWorkspace(mixedCasePath)).toBe(
+          true,
+        );
+
+        // Case 1: Root is lower, Check is Upper
+        const upperPath = path.join(lowerCwd.toUpperCase(), 'FILE.TXT');
+        expect(workspaceContext.isPathWithinWorkspace(upperPath)).toBe(true);
+
+        // Case 2: Root is Upper, Check is Lower
+        // Use a mixed case directory to simulate case-insensitivity without hitting root-level EACCES
+        const mixedRoot = path.join(cwd, 'MixedCaseRoot');
+        if (!fs.existsSync(mixedRoot)) {
+          fs.mkdirSync(mixedRoot);
+        }
+        const workspaceContextMixed = new WorkspaceContext(mixedRoot);
+        const lowerPathValues = path.join(mixedRoot.toLowerCase(), 'file.txt');
+        expect(
+          workspaceContextMixed.isPathWithinWorkspace(lowerPathValues),
+        ).toBe(true);
+      } finally {
+        Object.defineProperty(process, 'platform', { value: originalPlatform });
+      }
+    });
+
     it('should handle nested directories correctly', () => {
       const workspaceContext = new WorkspaceContext(cwd, [otherDir]);
       const nestedPath = path.join(cwd, 'deeply', 'nested', 'path', 'file.txt');
diff --git a/packages/core/src/utils/workspaceContext.ts b/packages/core/src/utils/workspaceContext.ts
index dfb47ce3bec..94ccf2d8628 100755
--- a/packages/core/src/utils/workspaceContext.ts
+++ b/packages/core/src/utils/workspaceContext.ts
@@ -6,6 +6,7 @@
 
 import { isNodeError } from '../utils/errors.js';
 import * as fs from 'node:fs';
+import * as os from 'node:os';
 import * as path from 'node:path';
 import { debugLogger } from './debugLogger.js';
 
@@ -22,6 +23,7 @@ export interface AddDirectoriesResult {
  * in a single session.
  */
 export class WorkspaceContext {
+  readonly targetDir: string;
   private directories = new Set<string>();
   private initialDirectories: Set<string>;
   private readOnlyPaths = new Set<string>();
@@ -32,10 +34,13 @@ export class WorkspaceContext {
    * @param targetDir The initial working directory (usually cwd)
    * @param additionalDirectories Optional array of additional directories to include
    */
-  constructor(
-    readonly targetDir: string,
-    additionalDirectories: string[] = [],
-  ) {
+  constructor(targetDir: string, additionalDirectories: string[] = []) {
+    // Ensure targetDir is in original case from filesystem
+    try {
+      this.targetDir = fs.realpathSync(targetDir);
+    } catch {
+      this.targetDir = targetDir;
+    }
     this.addDirectory(targetDir);
     this.addDirectories(additionalDirectories);
     this.initialDirectories = new Set(this.directories);
@@ -228,7 +233,26 @@ export class WorkspaceContext {
    */
   private fullyResolvedPath(pathToCheck: string): string {
     try {
-      return fs.realpathSync(path.resolve(this.targetDir, pathToCheck));
+      let resolvedInput = path.resolve(this.targetDir, pathToCheck);
+
+      // On Windows, if pathToCheck is already absolute with incorrect casing, fix it
+      if (os.platform() === 'win32' && path.isAbsolute(pathToCheck)) {
+        try {
+          resolvedInput = fs.realpathSync(pathToCheck);
+        } catch {
+          // Normalize the case by matching against targetDir
+          const normalizedPathToCheck = pathToCheck.toLowerCase();
+          const normalizedTargetDir = this.targetDir.toLowerCase();
+
+          if (normalizedPathToCheck.startsWith(normalizedTargetDir)) {
+            resolvedInput =
+              this.targetDir +
+              pathToCheck.substring(normalizedTargetDir.length);
+          }
+        }
+      }
+
+      return fs.realpathSync(resolvedInput);
     } catch (e: unknown) {
       if (
         isNodeError(e) &&
@@ -255,7 +279,12 @@ export class WorkspaceContext {
     pathToCheck: string,
     rootDirectory: string,
   ): boolean {
-    const relative = path.relative(rootDirectory, pathToCheck);
+    const normalizedRoot =
+      os.platform() === 'win32' ? rootDirectory.toLowerCase() : rootDirectory;
+    const normalizedPath =
+      os.platform() === 'win32' ? pathToCheck.toLowerCase() : pathToCheck;
+
+    const relative = path.relative(normalizedRoot, normalizedPath);
     return (
       !relative.startsWith(`..${path.sep}`) &&
       relative !== '..' &&