diff --git a/src/cli/commands/plugin-skills.ts b/src/cli/commands/plugin-skills.ts
index 5c3d986..bffb669 100644
--- a/src/cli/commands/plugin-skills.ts
+++ b/src/cli/commands/plugin-skills.ts
@@ -5,9 +5,7 @@ import chalk from 'chalk';
 import { command, positional, option, flag, string, optional, restPositionals } from 'cmd-ts';
 import { syncWorkspace, syncUserWorkspace } from '../../core/sync.js';
 import {
-  addDisabledSkill,
   removeDisabledSkill,
-  removeEnabledSkill,
   addEnabledSkill,
   addPlugin,
   hasPlugin,
@@ -16,9 +14,7 @@ import {
   upsertGitHubPluginSourceAllowlist,
 } from '../../core/workspace-modify.js';
 import {
-  addUserDisabledSkill,
   removeUserDisabledSkill,
-  removeUserEnabledSkill,
   addUserEnabledSkill,
   isUserConfigPath,
   addUserPlugin,
@@ -55,6 +51,7 @@ import {
 } from '../../core/marketplace.js';
 import { parseMarketplaceManifest, resolvePluginSourcePath } from '../../utils/marketplace-manifest-parser.js';
 import { formatSyncHeader, formatSyncSummary, formatVerboseSyncLines } from '../format-sync.js';
+import { removeInstalledSkill } from '../skill-removal.js';
 import type { SyncResult } from '../../core/sync.js';
 
 /**
@@ -336,10 +333,10 @@ const removeCmd = command({
       const workspacePath = isUser ? getHomeDir() : process.cwd();
 
       // Find the skill
-      const matches = await findSkillByName(skill, workspacePath);
+      const allSkills = await getAllSkillsFromPlugins(workspacePath);
+      const matches = allSkills.filter((candidate) => candidate.name === skill);
 
       if (matches.length === 0) {
-        const allSkills = await getAllSkillsFromPlugins(workspacePath);
         const skillNames = [...new Set(allSkills.map((s) => s.name))].join(', ');
         const error = `Skill '${skill}' not found in any installed plugin.\n\nAvailable skills: ${skillNames || 'none'}`;
         if (isJsonMode()) {
@@ -391,12 +388,12 @@ const removeCmd = command({
         return;
       }
 
-      const skillKey = `${targetSkill.pluginName}:${skill}`;
-
-      const result = targetSkill.pluginSkillsMode === 'allowlist'
-        ? isUser ? await removeUserEnabledSkill(skillKey) : await removeEnabledSkill(skillKey, workspacePath)
-        : isUser ? await addUserDisabledSkill(skillKey) : await addDisabledSkill(skillKey, workspacePath);
-
+      const result = await removeInstalledSkill({
+        targetSkill,
+        isUser,
+        workspacePath,
+        allSkills,
+      });
       if (!result.success) {
         if (isJsonMode()) {
           jsonOutput({ success: false, command: 'skill remove', error: result.error ?? 'Unknown error' });
@@ -407,7 +404,13 @@ const removeCmd = command({
       }
 
       if (!isJsonMode()) {
-        console.log(`\u2713 Disabled skill: ${skill} (${targetSkill.pluginName})`);
+        if (result.action === 'removed-plugin') {
+          console.log(`\u2713 Removed plugin: ${targetSkill.pluginSource}`);
+        } else if (result.action === 'removed-skill') {
+          console.log(`\u2713 Removed skill: ${skill} (${targetSkill.pluginName})`);
+        } else {
+          console.log(`\u2713 Disabled skill: ${skill} (${targetSkill.pluginName})`);
+        }
       }
 
       const syncResult = isUser ? await syncUserWorkspace() : await syncWorkspace(workspacePath);
diff --git a/src/cli/skill-removal.ts b/src/cli/skill-removal.ts
new file mode 100644
index 0000000..e1cedb8
--- /dev/null
+++ b/src/cli/skill-removal.ts
@@ -0,0 +1,55 @@
+import { addDisabledSkill, removeEnabledSkill, removePlugin } from '../core/workspace-modify.js';
+import { getAllSkillsFromPlugins, type SkillInfo } from '../core/skills.js';
+import {
+  addUserDisabledSkill,
+  removeUserEnabledSkill,
+  removeUserPlugin,
+} from '../core/user-workspace.js';
+
+export interface RemoveInstalledSkillOptions {
+  targetSkill: Pick<SkillInfo, 'name' | 'pluginName' | 'pluginSource' | 'pluginSkillsMode'>;
+  isUser: boolean;
+  workspacePath: string;
+  allSkills?: SkillInfo[];
+}
+
+export interface RemoveInstalledSkillResult {
+  success: boolean;
+  error?: string;
+  action?: 'removed-plugin' | 'removed-skill' | 'disabled-skill';
+}
+
+export async function removeInstalledSkill(
+  options: RemoveInstalledSkillOptions,
+): Promise<RemoveInstalledSkillResult> {
+  const { targetSkill, isUser, workspacePath } = options;
+  const allSkills = options.allSkills ?? await getAllSkillsFromPlugins(workspacePath);
+  const pluginSkills = allSkills.filter((skill) => skill.pluginSource === targetSkill.pluginSource);
+  const remainingEnabledSkills = pluginSkills.filter(
+    (skill) => !skill.disabled && skill.name !== targetSkill.name,
+  );
+
+  if (remainingEnabledSkills.length === 0) {
+    const result = isUser
+      ? await removeUserPlugin(targetSkill.pluginSource)
+      : await removePlugin(targetSkill.pluginSource, workspacePath);
+
+    return result.success
+      ? { success: true, action: 'removed-plugin' }
+      : { success: false, error: result.error ?? 'Unknown error' };
+  }
+
+  const skillKey = `${targetSkill.pluginName}:${targetSkill.name}`;
+  const result = targetSkill.pluginSkillsMode === 'allowlist'
+    ? isUser ? await removeUserEnabledSkill(skillKey) : await removeEnabledSkill(skillKey, workspacePath)
+    : isUser ? await addUserDisabledSkill(skillKey) : await addDisabledSkill(skillKey, workspacePath);
+
+  if (!result.success) {
+    return { success: false, error: result.error ?? 'Unknown error' };
+  }
+
+  return {
+    success: true,
+    action: targetSkill.pluginSkillsMode === 'allowlist' ? 'removed-skill' : 'disabled-skill',
+  };
+}
diff --git a/src/cli/tui/actions/plugins.ts b/src/cli/tui/actions/plugins.ts
index b308ef1..ce80aa9 100644
--- a/src/cli/tui/actions/plugins.ts
+++ b/src/cli/tui/actions/plugins.ts
@@ -1,12 +1,10 @@
 import * as p from '@clack/prompts';
-import { addPlugin, removePlugin, addDisabledSkill, removeDisabledSkill, addEnabledSkill, removeEnabledSkill, setPluginSkillsMode } from '../../../core/workspace-modify.js';
+import { addPlugin, removePlugin, removeDisabledSkill, addEnabledSkill, setPluginSkillsMode } from '../../../core/workspace-modify.js';
 import {
   addUserPlugin,
   removeUserPlugin,
-  addUserDisabledSkill,
   removeUserDisabledSkill,
   addUserEnabledSkill,
-  removeUserEnabledSkill,
   setUserPluginSkillsMode,
   getInstalledUserPlugins,
   getInstalledProjectPlugins,
@@ -32,6 +30,7 @@ import { getAllSkillsFromPlugins, discoverSkillNames } from '../../../core/skill
 import { getHomeDir } from '../../../constants.js';
 import type { TuiContext } from '../context.js';
 import type { TuiCache } from '../cache.js';
+import { removeInstalledSkill } from '../../skill-removal.js';
 
 const { select, text, confirm, multiselect, autocomplete } = p;
 
@@ -565,20 +564,11 @@ export async function runBrowsePluginSkills(
 
     // Disable newly unchecked skills
     for (const skill of toDisable) {
-      const skillKey = `${skill.pluginName}:${skill.name}`;
-      if (skill.pluginSkillsMode === 'allowlist') {
-        if (scope === 'user') {
-          await removeUserEnabledSkill(skillKey);
-        } else if (context.workspacePath) {
-          await removeEnabledSkill(skillKey, context.workspacePath);
-        }
-      } else {
-        if (scope === 'user') {
-          await addUserDisabledSkill(skillKey);
-        } else if (context.workspacePath) {
-          await addDisabledSkill(skillKey, context.workspacePath);
-        }
-      }
+      await removeInstalledSkill({
+        targetSkill: skill,
+        isUser: scope === 'user',
+        workspacePath,
+      });
     }
 
     // Enable newly checked skills
diff --git a/src/cli/tui/actions/skills.ts b/src/cli/tui/actions/skills.ts
index fbe2808..faec2b7 100644
--- a/src/cli/tui/actions/skills.ts
+++ b/src/cli/tui/actions/skills.ts
@@ -1,17 +1,13 @@
 import * as p from '@clack/prompts';
 import { getAllSkillsFromPlugins, discoverSkillNames, type SkillInfo } from '../../../core/skills.js';
 import {
-  addDisabledSkill,
   removeDisabledSkill,
   addEnabledSkill,
-  removeEnabledSkill,
   hasPlugin,
 } from '../../../core/workspace-modify.js';
 import {
-  addUserDisabledSkill,
   removeUserDisabledSkill,
   addUserEnabledSkill,
-  removeUserEnabledSkill,
   isUserConfigPath,
   hasUserPlugin,
 } from '../../../core/user-workspace.js';
@@ -25,6 +21,7 @@ import { getHomeDir } from '../../../constants.js';
 import type { TuiContext } from '../context.js';
 import type { TuiCache } from '../cache.js';
 import { installSelectedPlugin, runBrowsePluginSkills } from './plugins.js';
+import { removeInstalledSkill } from '../../skill-removal.js';
 
 const { multiselect, select, autocomplete, text } = p;
 
@@ -223,18 +220,13 @@ async function runToggleSkills(
 
   // Disable newly unchecked skills
   for (const skill of toDisable) {
-    if (skill.pluginSkillsMode === 'allowlist') {
-      if (skill.scope === 'user') {
-        await removeUserEnabledSkill(skill.skillKey);
-      } else if (context.workspacePath) {
-        await removeEnabledSkill(skill.skillKey, context.workspacePath);
-      }
-    } else {
-      if (skill.scope === 'user') {
-        await addUserDisabledSkill(skill.skillKey);
-      } else if (context.workspacePath) {
-        await addDisabledSkill(skill.skillKey, context.workspacePath);
-      }
+    const effectivePath = skill.scope === 'user' ? getHomeDir() : context.workspacePath;
+    if (effectivePath) {
+      await removeInstalledSkill({
+        targetSkill: skill,
+        isUser: skill.scope === 'user',
+        workspacePath: effectivePath,
+      });
     }
     if (skill.scope === 'user') changedUser = true;
     else changedProject = true;
diff --git a/tests/unit/cli/skill-removal.test.ts b/tests/unit/cli/skill-removal.test.ts
new file mode 100644
index 0000000..ec8be60
--- /dev/null
+++ b/tests/unit/cli/skill-removal.test.ts
@@ -0,0 +1,213 @@
+import { describe, it, expect, beforeEach, afterEach } from 'bun:test';
+import { mkdtemp, mkdir, readFile, rm, writeFile } from 'node:fs/promises';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { load, dump } from 'js-yaml';
+import { removeInstalledSkill } from '../../../src/cli/skill-removal.js';
+import type { WorkspaceConfig } from '../../../src/models/workspace-config.js';
+import type { SkillInfo } from '../../../src/core/skills.js';
+import { resetFetchCache } from '../../../src/core/plugin.js';
+
+describe('removeInstalledSkill', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await mkdtemp(join(tmpdir(), 'allagents-skill-removal-'));
+    await mkdir(join(tmpDir, '.allagents'), { recursive: true });
+  });
+
+  afterEach(async () => {
+    resetFetchCache();
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  it('removes the plugin when removing its only installed skill', async () => {
+    const pluginDir = join(tmpDir, 'solo-plugin');
+    await mkdir(pluginDir, { recursive: true });
+    await writeFile(
+      join(pluginDir, 'SKILL.md'),
+      '---\nname: solo-skill\ndescription: Solo skill\n---\n# Solo skill\n',
+    );
+
+    const config: WorkspaceConfig = {
+      version: 2,
+      repositories: [],
+      clients: ['copilot'],
+      plugins: [{ source: pluginDir, skills: ['solo-skill'] }],
+    };
+    await writeFile(join(tmpDir, '.allagents/workspace.yaml'), dump(config), 'utf-8');
+
+    const result = await removeInstalledSkill({
+      targetSkill: {
+        name: 'solo-skill',
+        pluginName: 'solo-plugin',
+        pluginSource: pluginDir,
+        pluginSkillsMode: 'allowlist',
+      },
+      isUser: false,
+      workspacePath: tmpDir,
+    });
+
+    expect(result).toEqual({ success: true, action: 'removed-plugin' });
+
+    const content = await readFile(join(tmpDir, '.allagents/workspace.yaml'), 'utf-8');
+    const updated = load(content) as WorkspaceConfig;
+    expect(updated.plugins).toEqual([]);
+  });
+
+  it('removes only the selected skill when the plugin exposes multiple skills', async () => {
+    const pluginDir = join(tmpDir, 'multi-plugin');
+    await mkdir(join(pluginDir, 'skills/skill-a'), { recursive: true });
+    await mkdir(join(pluginDir, 'skills/skill-b'), { recursive: true });
+    await writeFile(
+      join(pluginDir, 'skills/skill-a/SKILL.md'),
+      '---\nname: skill-a\ndescription: Skill A\n---\n# Skill A\n',
+    );
+    await writeFile(
+      join(pluginDir, 'skills/skill-b/SKILL.md'),
+      '---\nname: skill-b\ndescription: Skill B\n---\n# Skill B\n',
+    );
+
+    const config: WorkspaceConfig = {
+      version: 2,
+      repositories: [],
+      clients: ['copilot'],
+      plugins: [{ source: pluginDir, skills: ['skill-a', 'skill-b'] }],
+    };
+    await writeFile(join(tmpDir, '.allagents/workspace.yaml'), dump(config), 'utf-8');
+
+    const allSkills: SkillInfo[] = [
+      {
+        name: 'skill-a',
+        pluginName: 'multi-plugin',
+        pluginSource: pluginDir,
+        path: join(pluginDir, 'skills/skill-a'),
+        disabled: false,
+        pluginSkillsMode: 'allowlist',
+      },
+      {
+        name: 'skill-b',
+        pluginName: 'multi-plugin',
+        pluginSource: pluginDir,
+        path: join(pluginDir, 'skills/skill-b'),
+        disabled: false,
+        pluginSkillsMode: 'allowlist',
+      },
+    ];
+
+    const result = await removeInstalledSkill({
+      targetSkill: allSkills[0]!,
+      isUser: false,
+      workspacePath: tmpDir,
+      allSkills,
+    });
+
+    expect(result).toEqual({ success: true, action: 'removed-skill' });
+
+    const content = await readFile(join(tmpDir, '.allagents/workspace.yaml'), 'utf-8');
+    const updated = load(content) as WorkspaceConfig;
+    expect(updated.plugins).toEqual([{ source: pluginDir, skills: ['skill-b'] }]);
+  });
+
+  it('removes the plugin when removing the last enabled skill from a multi-skill plugin', async () => {
+    const pluginDir = join(tmpDir, 'mixed-plugin');
+    await mkdir(join(pluginDir, 'skills/skill-a'), { recursive: true });
+    await mkdir(join(pluginDir, 'skills/skill-b'), { recursive: true });
+    await writeFile(
+      join(pluginDir, 'skills/skill-a/SKILL.md'),
+      '---\nname: skill-a\ndescription: Skill A\n---\n# Skill A\n',
+    );
+    await writeFile(
+      join(pluginDir, 'skills/skill-b/SKILL.md'),
+      '---\nname: skill-b\ndescription: Skill B\n---\n# Skill B\n',
+    );
+
+    const config: WorkspaceConfig = {
+      version: 2,
+      repositories: [],
+      clients: ['copilot'],
+      plugins: [{ source: pluginDir, skills: ['skill-a'] }],
+    };
+    await writeFile(join(tmpDir, '.allagents/workspace.yaml'), dump(config), 'utf-8');
+
+    const allSkills: SkillInfo[] = [
+      {
+        name: 'skill-a',
+        pluginName: 'mixed-plugin',
+        pluginSource: pluginDir,
+        path: join(pluginDir, 'skills/skill-a'),
+        disabled: false,
+        pluginSkillsMode: 'allowlist',
+      },
+      {
+        name: 'skill-b',
+        pluginName: 'mixed-plugin',
+        pluginSource: pluginDir,
+        path: join(pluginDir, 'skills/skill-b'),
+        disabled: true,
+        pluginSkillsMode: 'allowlist',
+      },
+    ];
+
+    const result = await removeInstalledSkill({
+      targetSkill: allSkills[0]!,
+      isUser: false,
+      workspacePath: tmpDir,
+      allSkills,
+    });
+
+    expect(result).toEqual({ success: true, action: 'removed-plugin' });
+
+    const content = await readFile(join(tmpDir, '.allagents/workspace.yaml'), 'utf-8');
+    const updated = load(content) as WorkspaceConfig;
+    expect(updated.plugins).toEqual([]);
+  });
+
+  it('removes a single-skill GitHub source instead of leaving an empty allowlist', async () => {
+    const originalHome = process.env.HOME;
+    const fakeHome = join(tmpDir, 'home');
+    const pluginDir = join(
+      fakeHome,
+      '.allagents/plugins/marketplaces/NousResearch-hermes-agent@main/skills/research/llm-wiki',
+    );
+    await mkdir(pluginDir, { recursive: true });
+    await writeFile(
+      join(pluginDir, 'SKILL.md'),
+      '---\nname: llm-wiki\ndescription: Wiki skill\n---\n# llm-wiki\n',
+    );
+
+    const source = 'https://github.com/NousResearch/hermes-agent/tree/main/skills/research/llm-wiki';
+    const config: WorkspaceConfig = {
+      version: 2,
+      repositories: [],
+      clients: ['copilot'],
+      plugins: [{ source, skills: ['llm-wiki'] }],
+    };
+    await writeFile(join(tmpDir, '.allagents/workspace.yaml'), dump(config), 'utf-8');
+
+    process.env.HOME = fakeHome;
+    resetFetchCache();
+
+    try {
+      const result = await removeInstalledSkill({
+        targetSkill: {
+          name: 'llm-wiki',
+          pluginName: 'llm-wiki',
+          pluginSource: source,
+          pluginSkillsMode: 'allowlist',
+        },
+        isUser: false,
+        workspacePath: tmpDir,
+      });
+
+      expect(result).toEqual({ success: true, action: 'removed-plugin' });
+
+      const content = await readFile(join(tmpDir, '.allagents/workspace.yaml'), 'utf-8');
+      const updated = load(content) as WorkspaceConfig;
+      expect(updated.plugins).toEqual([]);
+    } finally {
+      process.env.HOME = originalHome;
+      resetFetchCache();
+    }
+  });
+});