diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 11d4830cc..e4a4c60b8 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -2,6 +2,11 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- Fixed `omp setup python` to validate the same configured or discovered interpreter used by the Python eval runtime.
+
+
 ## [17.2.4] - 2026-08-01
 
 ### Added
diff --git a/packages/coding-agent/src/cli/setup-cli.ts b/packages/coding-agent/src/cli/setup-cli.ts
index 4f3be8f50..24d9cbb73 100644
--- a/packages/coding-agent/src/cli/setup-cli.ts
+++ b/packages/coding-agent/src/cli/setup-cli.ts
@@ -4,10 +4,10 @@
  * Handles `omp setup` for onboarding and `omp setup <component>` for optional dependencies.
  */
 import * as path from "node:path";
-import { $which, APP_NAME, getProjectDir, getPythonEnvDir } from "@oh-my-pi/pi-utils";
-import { $ } from "bun";
+import { APP_NAME, getProjectDir, getPythonEnvDir } from "@oh-my-pi/pi-utils";
 import chalk from "chalk";
 import { Settings, settings } from "../config/settings";
+import { checkPythonKernelAvailability } from "../eval/py/kernel";
 import { theme } from "../modes/theme/theme";
 import { downloadSttModel, isSttModelCached } from "../stt/downloader";
 import { isSttModelKey, STT_MODEL_OPTIONS } from "../stt/models";
@@ -82,25 +82,14 @@ function managedPythonPath(): string {
 /**
  * Check Python environment and kernel dependencies.
  */
-async function checkPythonSetup(): Promise<PythonCheckResult> {
-	const result: PythonCheckResult = {
-		available: false,
+async function checkPythonSetup(cwd: string, interpreter?: string): Promise<PythonCheckResult> {
+	const availability = await checkPythonKernelAvailability(cwd, interpreter);
+	return {
+		available: availability.ok,
+		pythonPath: availability.pythonPath,
+		usingManagedEnv: availability.pythonPath === managedPythonPath(),
 		managedEnvPath: MANAGED_PYTHON_ENV,
 	};
-
-	const systemPythonPath = $which("python") ?? $which("python3");
-	const managedPath = managedPythonPath();
-	const hasManagedEnv = await Bun.file(managedPath).exists();
-
-	const pythonPath = systemPythonPath ?? (hasManagedEnv ? managedPath : undefined);
-	if (!pythonPath) {
-		return result;
-	}
-	const probe = await $`${pythonPath} -c "import sys;sys.exit(0)"`.quiet().nothrow();
-	result.pythonPath = pythonPath;
-	result.available = probe.exitCode === 0;
-	result.usingManagedEnv = pythonPath === managedPath;
-	return result;
 }
 
 /**
@@ -126,7 +115,10 @@ export async function runSetupCommand(cmd: SetupCommandArgs): Promise<void> {
 }
 
 async function handlePythonSetup(flags: { json?: boolean; check?: boolean }): Promise<void> {
-	const check = await checkPythonSetup();
+	const cwd = getProjectDir();
+	const projectSettings = await Settings.init({ cwd });
+	const interpreter = projectSettings.get("python.interpreter")?.trim() || undefined;
+	const check = await checkPythonSetup(cwd, interpreter);
 
 	if (flags.json) {
 		console.log(JSON.stringify(check, null, 2));
@@ -136,7 +128,7 @@ async function handlePythonSetup(flags: { json?: boolean; check?: boolean }): Pr
 
 	if (!check.pythonPath) {
 		console.error(chalk.red(`${theme.status.error} Python not found`));
-		console.error(chalk.dim("Install Python 3.8+ and ensure it's in your PATH"));
+		console.error(chalk.dim("Install Python 3.8+ or set python.interpreter to its executable path"));
 		process.exit(1);
 	}
 
diff --git a/packages/coding-agent/test/setup-cli.test.ts b/packages/coding-agent/test/setup-cli.test.ts
new file mode 100644
index 000000000..92834855a
--- /dev/null
+++ b/packages/coding-agent/test/setup-cli.test.ts
@@ -0,0 +1,81 @@
+import { afterEach, describe, expect, it } from "bun:test";
+import * as fs from "node:fs/promises";
+import * as path from "node:path";
+import { TempDir } from "@oh-my-pi/pi-utils";
+
+const cliEntry = path.join(import.meta.dir, "..", "src", "cli.ts");
+
+interface CliProcessResult {
+	exitCode: number;
+	output: string;
+	error: string;
+}
+
+async function runSetupPython(cwd: string): Promise<CliProcessResult> {
+	const env: NodeJS.ProcessEnv = {
+		...process.env,
+		NO_COLOR: "1",
+		PI_CODING_AGENT_DIR: path.join(cwd, "agent"),
+	};
+	delete env.VIRTUAL_ENV;
+	delete env.CONDA_DEFAULT_ENV;
+	delete env.CONDA_PREFIX;
+	const proc = Bun.spawn([process.execPath, cliEntry, "setup", "python", "--json"], {
+		cwd,
+		stdout: "pipe",
+		stderr: "pipe",
+		env,
+	});
+	const output = new Response(proc.stdout).text();
+	const error = new Response(proc.stderr).text();
+	const [exitCode, stdout, stderr] = await Promise.all([proc.exited, output, error]);
+	return { exitCode, output: stdout, error: stderr };
+}
+
+describe("omp setup python", () => {
+	let projectDir: TempDir | undefined;
+
+	afterEach(async () => {
+		await projectDir?.remove();
+		projectDir = undefined;
+	});
+
+	it.skipIf(process.platform === "win32")(
+		"probes the project-configured interpreter instead of the PATH interpreter",
+		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 0\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);
+
+			expect(result.error).toBe("");
+			expect(result.exitCode).toBe(0);
+			expect(JSON.parse(result.output)).toMatchObject({
+				available: true,
+				pythonPath: interpreter,
+				usingManagedEnv: false,
+			});
+		},
+	);
+	it.skipIf(process.platform === "win32")("prefers the project venv over the PATH interpreter", async () => {
+		projectDir = TempDir.createSync("@omp-setup-python-");
+		const cwd = projectDir.path();
+		const interpreter = path.join(cwd, ".venv", "bin", "python");
+		await Bun.write(interpreter, "#!/bin/sh\nexit 0\n");
+		await fs.chmod(interpreter, 0o755);
+
+		const result = await runSetupPython(cwd);
+
+		expect(result.error).toBe("");
+		expect(result.exitCode).toBe(0);
+		expect(JSON.parse(result.output)).toMatchObject({
+			available: true,
+			pythonPath: interpreter,
+			usingManagedEnv: false,
+		});
+	});
+});