diff --git a/.changeset/cli-hidden-commands.md b/.changeset/cli-hidden-commands.md
new file mode 100644
index 0000000000..57d7468cc8
--- /dev/null
+++ b/.changeset/cli-hidden-commands.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': patch
+---
+
+Internal refactor of the CLI command registration
diff --git a/packages/cli/src/wiring/CliInitializer.test.ts b/packages/cli/src/wiring/CliInitializer.test.ts
index e04a429ede..10de6d8e09 100644
--- a/packages/cli/src/wiring/CliInitializer.test.ts
+++ b/packages/cli/src/wiring/CliInitializer.test.ts
@@ -92,6 +92,124 @@ describe('CliInitializer', () => {
     expect(process.exit).toHaveBeenCalledWith(0);
   });
 
+  it('should run experimental commands but exclude them from help output', async () => {
+    expect.assertions(3);
+    process.argv = ['node', 'cli', 'secret'];
+    const initializer = new CliInitializer();
+    initializer.add(
+      createCliPlugin({
+        pluginId: 'test',
+        init: async reg => {
+          reg.addCommand({
+            path: ['visible'],
+            description: 'A visible command',
+            execute: () => Promise.resolve(),
+          });
+          reg.addCommand({
+            path: ['secret'],
+            description: 'An experimental command',
+            experimental: true,
+            execute: ({ args }) => {
+              expect(args).toEqual([]);
+              return Promise.resolve();
+            },
+          });
+        },
+      }),
+    );
+    await initializer.run();
+    expect(process.exit).toHaveBeenCalledWith(0);
+
+    process.argv = ['node', 'cli', '--help'];
+    const writeSpy = jest.spyOn(process.stdout, 'write');
+    const initializer2 = new CliInitializer();
+    initializer2.add(
+      createCliPlugin({
+        pluginId: 'test',
+        init: async reg => {
+          reg.addCommand({
+            path: ['visible'],
+            description: 'A visible command',
+            execute: () => Promise.resolve(),
+          });
+          reg.addCommand({
+            path: ['secret'],
+            description: 'An experimental command',
+            experimental: true,
+            execute: () => Promise.resolve(),
+          });
+        },
+      }),
+    );
+    await initializer2.run();
+    const helpOutput = writeSpy.mock.calls.map(c => c[0]).join('');
+    expect(helpOutput).not.toContain('secret');
+    writeSpy.mockRestore();
+  });
+
+  it('should hide tree nodes when all children are experimental', async () => {
+    process.argv = ['node', 'cli', '--help'];
+    const writeSpy = jest.spyOn(process.stdout, 'write');
+    const initializer = new CliInitializer();
+    initializer.add(
+      createCliPlugin({
+        pluginId: 'test',
+        init: async reg => {
+          reg.addCommand({
+            path: ['visible'],
+            description: 'A visible command',
+            execute: () => Promise.resolve(),
+          });
+          reg.addCommand({
+            path: ['group', 'alpha'],
+            description: 'First experimental command',
+            experimental: true,
+            execute: () => Promise.resolve(),
+          });
+          reg.addCommand({
+            path: ['group', 'beta'],
+            description: 'Second experimental command',
+            experimental: true,
+            execute: () => Promise.resolve(),
+          });
+        },
+      }),
+    );
+    await initializer.run();
+    const helpOutput = writeSpy.mock.calls.map(c => c[0]).join('');
+    expect(helpOutput).toContain('visible');
+    expect(helpOutput).not.toContain('group');
+    writeSpy.mockRestore();
+  });
+
+  it('should show tree nodes when some children are visible', async () => {
+    process.argv = ['node', 'cli', '--help'];
+    const writeSpy = jest.spyOn(process.stdout, 'write');
+    const initializer = new CliInitializer();
+    initializer.add(
+      createCliPlugin({
+        pluginId: 'test',
+        init: async reg => {
+          reg.addCommand({
+            path: ['group', 'alpha'],
+            description: 'A visible nested command',
+            execute: () => Promise.resolve(),
+          });
+          reg.addCommand({
+            path: ['group', 'beta'],
+            description: 'An experimental nested command',
+            experimental: true,
+            execute: () => Promise.resolve(),
+          });
+        },
+      }),
+    );
+    await initializer.run();
+    const helpOutput = writeSpy.mock.calls.map(c => c[0]).join('');
+    expect(helpOutput).toContain('group');
+    writeSpy.mockRestore();
+  });
+
   it('should pass positional args to the subcommand if nested', async () => {
     expect.assertions(2);
     process.argv = [
diff --git a/packages/cli/src/wiring/CliInitializer.ts b/packages/cli/src/wiring/CliInitializer.ts
index c07fbb26f3..d9af1e8a4d 100644
--- a/packages/cli/src/wiring/CliInitializer.ts
+++ b/packages/cli/src/wiring/CliInitializer.ts
@@ -15,7 +15,7 @@
  */
 
 import { CommandGraph } from './CommandGraph';
-import { CliFeature, OpaqueCliPlugin } from './types';
+import { BackstageCommand, CliFeature, OpaqueCliPlugin } from './types';
 import { CommandRegistry } from './CommandRegistry';
 import { Command } from 'commander';
 import { version } from './version';
@@ -24,6 +24,17 @@ import { exitWithError } from './errors';
 import { ForwardedError } from '@backstage/errors';
 import { isPromise } from 'node:util/types';
 
+function isNodeHidden(
+  node:
+    | { $$type: '@tree/leaf'; command: BackstageCommand }
+    | { $$type: '@tree/root'; children: unknown[] },
+): boolean {
+  if (node.$$type === '@tree/leaf') {
+    return !!node.command.deprecated || !!node.command.experimental;
+  }
+  return node.children.every(child => isNodeHidden(child as any));
+}
+
 type UninitializedFeature = CliFeature | Promise<{ default: CliFeature }>;
 
 export class CliInitializer {
@@ -80,7 +91,9 @@ export class CliInitializer {
       const { node, argParser } = queue.shift()!;
       if (node.$$type === '@tree/root') {
         const treeParser = argParser
-          .command(`${node.name} [command]`)
+          .command(`${node.name} [command]`, {
+            hidden: isNodeHidden(node),
+          })
           .description(node.name);
 
         queue.push(
@@ -91,7 +104,9 @@ export class CliInitializer {
         );
       } else {
         argParser
-          .command(node.name, { hidden: !!node.command.deprecated })
+          .command(node.name, {
+            hidden: !!node.command.deprecated || !!node.command.experimental,
+          })
           .description(node.command.description)
           .helpOption(false)
           .allowUnknownOption(true)
diff --git a/packages/cli/src/wiring/types.ts b/packages/cli/src/wiring/types.ts
index e0f697990f..fa3d2341f0 100644
--- a/packages/cli/src/wiring/types.ts
+++ b/packages/cli/src/wiring/types.ts
@@ -35,6 +35,7 @@ export interface BackstageCommand {
   path: string[];
   description: string;
   deprecated?: boolean;
+  experimental?: boolean;
   execute:
     | CommandExecuteFn
     | {