diff --git a/src/features/skill-mcp-manager/env-cleaner.test.ts b/src/features/skill-mcp-manager/env-cleaner.test.ts
index 75cfe348e..0a0b4f6df 100644
--- a/src/features/skill-mcp-manager/env-cleaner.test.ts
+++ b/src/features/skill-mcp-manager/env-cleaner.test.ts
@@ -112,8 +112,8 @@ describe("createCleanMcpEnvironment", () => {
       process.env.PATH = "/usr/bin"
       process.env.NPM_CONFIG_REGISTRY = "https://private.registry.com"
       const customEnv = {
-        MCP_API_KEY: "secret-key",
-        CUSTOM_VAR: "custom-value",
+        SAFE_CUSTOM_VAR: "custom-value",
+        ANOTHER_SAFE_VAR: "another-value",
       }
 
       // when
@@ -122,8 +122,8 @@ describe("createCleanMcpEnvironment", () => {
       // then
       expect(cleanEnv.PATH).toBe("/usr/bin")
       expect(cleanEnv.NPM_CONFIG_REGISTRY).toBeUndefined()
-      expect(cleanEnv.MCP_API_KEY).toBe("secret-key")
-      expect(cleanEnv.CUSTOM_VAR).toBe("custom-value")
+      expect(cleanEnv.SAFE_CUSTOM_VAR).toBe("custom-value")
+      expect(cleanEnv.ANOTHER_SAFE_VAR).toBe("another-value")
     })
 
     it("custom env can override process.env values", () => {
@@ -139,6 +139,25 @@ describe("createCleanMcpEnvironment", () => {
       // then
       expect(cleanEnv.NODE_ENV).toBe("production")
     })
+
+    it("filters secret keys from customEnv that would bypass process.env filtering", () => {
+      // given - customEnv tries to inject secrets that should be filtered
+      process.env.PATH = "/usr/bin"
+      const customEnv = {
+        MCP_API_KEY: "secret-key-that-should-be-filtered",
+        CUSTOM_SECRET: "another-secret",
+        SAFE_VAR: "safe-value",
+      }
+
+      // when
+      const cleanEnv = createCleanMcpEnvironment(customEnv)
+
+      // then - secret keys from customEnv are filtered despite not being in process.env
+      expect(cleanEnv.MCP_API_KEY).toBeUndefined()
+      expect(cleanEnv.CUSTOM_SECRET).toBeUndefined()
+      expect(cleanEnv.SAFE_VAR).toBe("safe-value")
+      expect(cleanEnv.PATH).toBe("/usr/bin")
+    })
   })
 
   describe("undefined value handling", () => {
diff --git a/src/features/skill-mcp-manager/env-cleaner.ts b/src/features/skill-mcp-manager/env-cleaner.ts
index 9c6ebe1aa..b5281c88a 100644
--- a/src/features/skill-mcp-manager/env-cleaner.ts
+++ b/src/features/skill-mcp-manager/env-cleaner.ts
@@ -28,18 +28,22 @@ export const EXCLUDED_ENV_PATTERNS: RegExp[] = [
 export function createCleanMcpEnvironment(
   customEnv: Record<string, string> = {}
 ): Record<string, string> {
-  const cleanEnv: Record<string, string> = {}
+  const mergedEnv: Record<string, string> = {}
 
   for (const [key, value] of Object.entries(process.env)) {
     if (value === undefined) continue
+    mergedEnv[key] = value
+  }
 
+  Object.assign(mergedEnv, customEnv)
+
+  const cleanEnv: Record<string, string> = {}
+  for (const [key, value] of Object.entries(mergedEnv)) {
     const shouldExclude = EXCLUDED_ENV_PATTERNS.some((pattern) => pattern.test(key))
     if (!shouldExclude) {
       cleanEnv[key] = value
     }
   }
 
-  Object.assign(cleanEnv, customEnv)
-
   return cleanEnv
 }