diff --git a/.github/workflows/sync_dependabot-changesets.yml b/.github/workflows/sync_dependabot-changesets.yml
index ef0efe04f9..2974407872 100644
--- a/.github/workflows/sync_dependabot-changesets.yml
+++ b/.github/workflows/sync_dependabot-changesets.yml
@@ -29,11 +29,23 @@ jobs:
         uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
         with:
           node-version: 20
-      - name: Dedupe lockfile
+      - name: Dedupe lockfiles
         run: |
           corepack enable
-          yarn dedupe
-          git add yarn.lock
+
+          # Root lockfile (Yarn 4)
+          if git diff --name-only HEAD~1 | grep -q '^yarn\.lock$'; then
+            yarn dedupe
+            git add yarn.lock
+          fi
+
+          # Subdirectory lockfiles (Yarn Classic)
+          for dir in docs-ui microsite; do
+            if git diff --name-only HEAD~1 | grep -q "^${dir}/yarn.lock$"; then
+              npx yarn-deduplicate "$dir/yarn.lock"
+              git add "$dir/yarn.lock"
+            fi
+          done
       - name: Generate changeset
         uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with: