diff --git a/index.cjs b/index.cjs
index 2a23b7ff0..fbdbafcb3 100644
--- a/index.cjs
+++ b/index.cjs
@@ -1180,11 +1180,35 @@ if (cmd === 'import') {
     fs.writeFileSync(path.join(agentDir, 'history.md'), historyContent);
   }
 
-  // Write skills
-  for (const skillContent of manifest.skills) {
+  // Write skills to .copilot/skills/ (the canonical location)
+  const copilotSkillsImportDir = path.join(dest, '.copilot', 'skills');
+  const importedSkills = manifest.skills.map((skillContent, index) => {
     const nameMatch = skillContent.match(/^name:\s*["']?(.+?)["']?\s*$/m);
-    const skillName = nameMatch ? nameMatch[1].trim().toLowerCase().replace(/\s+/g, '-') : `skill-${manifest.skills.indexOf(skillContent)}`;
-    const skillDir = path.join(aiTeamDir, 'skills', skillName);
+    const skillName = nameMatch
+      ? nameMatch[1].trim().toLowerCase().replace(/\s+/g, '-')
+      : `skill-${index}`;
+    return { skillContent, skillName };
+  });
+  const hasForce = typeof force !== 'undefined' && force;
+
+  if (fs.existsSync(copilotSkillsImportDir)) {
+    if (hasForce) {
+      const archivedSkillsDir = path.join(dest, '.copilot', `skills.backup.${Date.now()}`);
+      fs.renameSync(copilotSkillsImportDir, archivedSkillsDir);
+    } else {
+      const collidingSkills = importedSkills
+        .map(({ skillName }) => skillName)
+        .filter((skillName) => fs.existsSync(path.join(copilotSkillsImportDir, skillName)));
+
+      if (collidingSkills.length > 0) {
+        fatal(`Import would overwrite existing Copilot skills: ${collidingSkills.join(', ')}. Re-run with --force to replace the existing .copilot/skills directory.`);
+      }
+    }
+  }
+
+  fs.mkdirSync(copilotSkillsImportDir, { recursive: true });
+  for (const { skillContent, skillName } of importedSkills) {
+    const skillDir = path.join(copilotSkillsImportDir, skillName);
     fs.mkdirSync(skillDir, { recursive: true });
     fs.writeFileSync(path.join(skillDir, 'SKILL.md'), skillContent);
   }