diff --git a/packages/coding-agent/src/cli/setup-cli.ts b/packages/coding-agent/src/cli/setup-cli.ts
index 24d9cbb73..1b4493112 100644
--- a/packages/coding-agent/src/cli/setup-cli.ts
+++ b/packages/coding-agent/src/cli/setup-cli.ts
@@ -83,7 +83,7 @@ function managedPythonPath(): string {
  * Check Python environment and kernel dependencies.
  */
 async function checkPythonSetup(cwd: string, interpreter?: string): Promise<PythonCheckResult> {
-	const availability = await checkPythonKernelAvailability(cwd, interpreter);
+	const availability = await checkPythonKernelAvailability(cwd, interpreter, { forceProbe: true });
 	return {
 		available: availability.ok,
 		pythonPath: availability.pythonPath,
diff --git a/packages/coding-agent/src/eval/py/kernel.ts b/packages/coding-agent/src/eval/py/kernel.ts
index 945db5561..82b19a1e9 100644
--- a/packages/coding-agent/src/eval/py/kernel.ts
+++ b/packages/coding-agent/src/eval/py/kernel.ts
@@ -82,8 +82,9 @@ const availabilityCache = new Map<string, Promise<PythonKernelAvailability>>();
 export async function checkPythonKernelAvailability(
 	cwd: string,
 	interpreter?: string,
+	options?: { forceProbe?: boolean },
 ): Promise<PythonKernelAvailability> {
-	if (isBunTestRuntime() || $flag("PI_PYTHON_SKIP_CHECK")) {
+	if (!options?.forceProbe && (isBunTestRuntime() || $flag("PI_PYTHON_SKIP_CHECK"))) {
 		return { ok: true };
 	}
 	const resolvedCwd = path.resolve(cwd);
diff --git a/packages/coding-agent/test/setup-cli.test.ts b/packages/coding-agent/test/setup-cli.test.ts
index 92834855a..c1a35a18f 100644
--- a/packages/coding-agent/test/setup-cli.test.ts
+++ b/packages/coding-agent/test/setup-cli.test.ts
@@ -11,11 +11,12 @@ interface CliProcessResult {
 	error: string;
 }
 
-async function runSetupPython(cwd: string): Promise<CliProcessResult> {
+async function runSetupPython(cwd: string, envOverrides?: NodeJS.ProcessEnv): Promise<CliProcessResult> {
 	const env: NodeJS.ProcessEnv = {
 		...process.env,
 		NO_COLOR: "1",
 		PI_CODING_AGENT_DIR: path.join(cwd, "agent"),
+		...envOverrides,
 	};
 	delete env.VIRTUAL_ENV;
 	delete env.CONDA_DEFAULT_ENV;
@@ -78,4 +79,22 @@ describe("omp setup python", () => {
 			usingManagedEnv: false,
 		});
 	});
+	it.skipIf(process.platform === "win32")("does not let the global probe bypass skip setup validation", async () => {
+		projectDir = TempDir.createSync("@omp-setup-python-");
+		const cwd = projectDir.path();
+		const interpreter = path.join(cwd, "configured-python");
+		await Bun.write(interpreter, "#!/bin/sh\nexit 23\n");
+		await fs.chmod(interpreter, 0o755);
+		await Bun.write(path.join(cwd, ".omp", "config.yml"), `python:\n  interpreter: ${interpreter}\n`);
+
+		const result = await runSetupPython(cwd, { PI_PYTHON_SKIP_CHECK: "1" });
+
+		expect(result.error).toBe("");
+		expect(result.exitCode).toBe(1);
+		expect(JSON.parse(result.output)).toMatchObject({
+			available: false,
+			pythonPath: interpreter,
+			usingManagedEnv: false,
+		});
+	});
 });