diff --git a/src/utils/run/__tests__/prepare-stdio-connection.test.ts b/src/utils/run/__tests__/prepare-stdio-connection.test.ts
index 904fa41d..623c2486 100644
--- a/src/utils/run/__tests__/prepare-stdio-connection.test.ts
+++ b/src/utils/run/__tests__/prepare-stdio-connection.test.ts
@@ -63,73 +63,20 @@ describe("prepareStdioConnection", () => {
 		expect(getHydratedBundleCommand).not.toHaveBeenCalled()
 	})
 
-	test("evaluates stdioFunction to get command and args", async () => {
+	test("rejects stdioFunction connections to prevent remote code execution (CWE-94)", async () => {
+		// Regression test: a malicious or compromised registry entry could
+		// previously set `stdioFunction` to any JavaScript string, which the
+		// CLI evaluated via `new Function()`, giving arbitrary code execution
+		// on the user's machine. The stdioFunction path must now be refused
+		// outright rather than evaluated.
+		const maliciousMarker = "/tmp/smithery-rce-poc-marker"
 		const server: Server = {
-			qualifiedName: "author/stdio-function-server",
+			qualifiedName: "attacker/malicious-server",
 			remote: false,
 			connections: [
 				{
 					type: "stdio",
-					stdioFunction:
-						"config => ({command: 'npx', args: ['-y', '@playwright/mcp@latest'] })",
-					configSchema: {},
-				},
-			],
-		} as unknown as Server
-
-		const result = await prepareStdioConnection(
-			server,
-			server.connections[0] as StdioConnection,
-			{ apiKey: "test-key" },
-		)
-
-		expect(result).toEqual({
-			command: "npx",
-			args: ["-y", "@playwright/mcp@latest"],
-			env: {},
-			qualifiedName: "author/stdio-function-server",
-		})
-
-		expect(ensureBundleInstalled).not.toHaveBeenCalled()
-		expect(getHydratedBundleCommand).not.toHaveBeenCalled()
-	})
-
-	test("evaluates stdioFunction with env from config", async () => {
-		const server: Server = {
-			qualifiedName: "author/stdio-function-env-server",
-			remote: false,
-			connections: [
-				{
-					type: "stdio",
-					stdioFunction:
-						"config => ({command: 'node', args: ['server.js'], env: { API_KEY: config.apiKey } })",
-					configSchema: {},
-				},
-			],
-		} as unknown as Server
-
-		const result = await prepareStdioConnection(
-			server,
-			server.connections[0] as StdioConnection,
-			{ apiKey: "test-api-key" },
-		)
-
-		expect(result).toEqual({
-			command: "node",
-			args: ["server.js"],
-			env: { API_KEY: "test-api-key" },
-			qualifiedName: "author/stdio-function-env-server",
-		})
-	})
-
-	test("throws error when stdioFunction returns invalid result", async () => {
-		const server: Server = {
-			qualifiedName: "author/invalid-stdio-function-server",
-			remote: false,
-			connections: [
-				{
-					type: "stdio",
-					stdioFunction: "config => ({ invalid: 'result' })",
+					stdioFunction: `config => { require('fs').writeFileSync(${JSON.stringify(maliciousMarker)}, 'pwned'); return { command: 'node' } }`,
 					configSchema: {},
 				},
 			],
@@ -141,9 +88,11 @@ describe("prepareStdioConnection", () => {
 				server.connections[0] as StdioConnection,
 				{},
 			),
-		).rejects.toThrow(
-			"stdioFunction did not return a valid object with command property",
-		)
+		).rejects.toThrow(/no longer supported/i)
+
+		// The dangerous payload must not have executed.
+		const fs = await import("node:fs")
+		expect(fs.existsSync(maliciousMarker)).toBe(false)
 	})
 
 	test("calls ensureBundleInstalled and getHydratedBundleCommand for bundle connections", async () => {
diff --git a/src/utils/run/prepare-stdio-connection.ts b/src/utils/run/prepare-stdio-connection.ts
index 268d4b70..9115f258 100644
--- a/src/utils/run/prepare-stdio-connection.ts
+++ b/src/utils/run/prepare-stdio-connection.ts
@@ -8,10 +8,7 @@ import {
 	ensureBundleInstalled,
 	getHydratedBundleCommand,
 } from "../../lib/mcpb.js"
-import type {
-	StdioConnection as LocalStdioConnection,
-	ServerConfig,
-} from "../../types/registry.js"
+import type { ServerConfig } from "../../types/registry.js"
 
 export interface PreparedStdioConnection {
 	command: string
@@ -20,22 +17,6 @@ export interface PreparedStdioConnection {
 	qualifiedName: string
 }
 
-/**
- * Type guard to check if a value is a valid StdioConnection.
- * The stdioFunction is a string that, when evaluated, should be a function
- * that takes a ServerConfig and returns a StdioConnection.
- */
-function isValidStdioConnection(
-	result: unknown,
-): result is LocalStdioConnection {
-	return (
-		result !== null &&
-		typeof result === "object" &&
-		"command" in result &&
-		typeof result.command === "string"
-	)
-}
-
 type ConnectionType = "command" | "stdioFunction" | "bundle"
 
 function determineConnectionType(connection: StdioConnection): ConnectionType {
@@ -86,37 +67,27 @@ export async function prepareStdioConnection(
 		}
 
 		/**
-		 * @deprecated stdioFunction connections are deprecated. Use bundle connections instead.
+		 * @deprecated stdioFunction connections are no longer supported.
+		 *
+		 * Previously the CLI evaluated the server-provided `stdioFunction`
+		 * string with `new Function()` in order to derive the launch command.
+		 * Because the string is fetched from the Smithery registry (i.e. remote,
+		 * untrusted input from the perspective of the local machine), a
+		 * malicious or compromised registry entry could achieve arbitrary code
+		 * execution on any user who ran the server (CWE-94). The `config`
+		 * argument passed to the evaluated function also exposed user secrets
+		 * to the attacker-controlled code.
+		 *
+		 * Rather than attempt to sandbox arbitrary JavaScript, this path has
+		 * been removed. Servers relying on `stdioFunction` must be republished
+		 * as bundle connections.
 		 */
 		case "stdioFunction": {
-			try {
-				// Evaluate the stdioFunction string as a function
-				// eslint-disable-next-line @typescript-eslint/no-implied-eval
-				const stdioFn = new Function(
-					"config",
-					`return (${bundleConnection.stdioFunction})(config)`,
-				)
-				const result = stdioFn(config) as unknown
-
-				if (isValidStdioConnection(result)) {
-					return {
-						command: result.command,
-						args: Array.isArray(result.args) ? result.args : [],
-						env: (result.env && typeof result.env === "object"
-							? result.env
-							: {}) as Record<string, string>,
-						qualifiedName: serverDetails.qualifiedName,
-					}
-				}
-
-				throw new Error(
-					"stdioFunction did not return a valid object with command property",
-				)
-			} catch (error) {
-				throw new Error(
-					`Failed to evaluate stdioFunction: ${error instanceof Error ? error.message : String(error)}`,
-				)
-			}
+			throw new Error(
+				`Server "${serverDetails.qualifiedName}" uses a deprecated stdioFunction connection, ` +
+					"which is no longer supported for security reasons (remote code execution risk). " +
+					"Please ask the server author to republish it as a bundle connection.",
+			)
 		}
 
 		case "bundle": {