diff --git a/src/commands/update.ts b/src/commands/update.ts
index 90664a7..e2b03de 100644
--- a/src/commands/update.ts
+++ b/src/commands/update.ts
@@ -13,7 +13,7 @@ import { readSkillMetadata, writeSkillMetadata } from '../utils/skill-metadata.j
  */
 export async function updateSkills(skillNames: string[] | string | undefined): Promise<void> {
   const requested = normalizeSkillNames(skillNames);
-  const skills = findAllSkills();
+  const skills = findAllSkills({ dedupe: false });
 
   if (skills.length === 0) {
     console.log('No skills installed.\n');
diff --git a/src/utils/skills.ts b/src/utils/skills.ts
index d3c8253..81563c8 100644
--- a/src/utils/skills.ts
+++ b/src/utils/skills.ts
@@ -27,9 +27,10 @@ function isDirectoryOrSymlinkToDirectory(entry: Dirent, parentDir: string): bool
 /**
  * Find all installed skills across directories
  */
-export function findAllSkills(): Skill[] {
+export function findAllSkills(options: { dedupe?: boolean } = {}): Skill[] {
   const skills: Skill[] = [];
   const seen = new Set<string>();
+  const dedupe = options.dedupe ?? true;
   const dirs = getSearchDirs();
 
   for (const dir of dirs) {
@@ -40,7 +41,7 @@ export function findAllSkills(): Skill[] {
     for (const entry of entries) {
       if (isDirectoryOrSymlinkToDirectory(entry, dir)) {
         // Deduplicate: only add if we haven't seen this skill name yet
-        if (seen.has(entry.name)) continue;
+        if (dedupe && seen.has(entry.name)) continue;
 
         const skillPath = join(dir, entry.name, 'SKILL.md');
         if (existsSync(skillPath)) {
diff --git a/tests/commands/update.test.ts b/tests/commands/update.test.ts
index 41f7568..ac4e95d 100644
--- a/tests/commands/update.test.ts
+++ b/tests/commands/update.test.ts
@@ -72,4 +72,45 @@ describe('updateSkills', () => {
     const content = readFileSync(join(targetDir, 'SKILL.md'), 'utf-8');
     expect(content).toContain('v1');
   });
+
+  it('updates all installed instances of the same skill name', async () => {
+    const sourceDir = join(tempRoot, 'source-multi');
+    mkdirSync(sourceDir, { recursive: true });
+    writeFileSync(
+      join(sourceDir, 'SKILL.md'),
+      "---\nname: demo\ndescription: v2\n---\n\n# Demo\nv2\n"
+    );
+
+    const projectTarget = join(projectDir, '.claude/skills/demo');
+    const globalTarget = join(process.env.HOME!, '.agent/skills/demo');
+    mkdirSync(projectTarget, { recursive: true });
+    mkdirSync(globalTarget, { recursive: true });
+
+    writeFileSync(
+      join(projectTarget, 'SKILL.md'),
+      "---\nname: demo\ndescription: v1\n---\n\n# Demo\nproject-v1\n"
+    );
+    writeFileSync(
+      join(globalTarget, 'SKILL.md'),
+      "---\nname: demo\ndescription: v1\n---\n\n# Demo\nglobal-v1\n"
+    );
+
+    writeSkillMetadata(projectTarget, {
+      source: './source-multi',
+      sourceType: 'local',
+      localPath: sourceDir,
+      installedAt: '2026-01-01T00:00:00.000Z',
+    });
+    writeSkillMetadata(globalTarget, {
+      source: './source-multi',
+      sourceType: 'local',
+      localPath: sourceDir,
+      installedAt: '2026-01-01T00:00:00.000Z',
+    });
+
+    await updateSkills(['demo']);
+
+    expect(readFileSync(join(projectTarget, 'SKILL.md'), 'utf-8')).toContain('v2');
+    expect(readFileSync(join(globalTarget, 'SKILL.md'), 'utf-8')).toContain('v2');
+  });
 });