diff --git a/.github/workflows/backend-ci.yml b/.github/workflows/backend-ci.yml
index e9d9d5a4..92b57682 100644
--- a/.github/workflows/backend-ci.yml
+++ b/.github/workflows/backend-ci.yml
@@ -26,6 +26,7 @@ jobs:
         - name: Upload coverage reports to Codecov
           uses: codecov/codecov-action@v4
           with:
-            directory: chartlets.py/
+            directory: chartlets.py/coverage/
+            flags: backend
             verbose: true
             token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/frontend-ci.yml b/.github/workflows/frontend-ci.yml
index e0f714d2..357ec783 100644
--- a/.github/workflows/frontend-ci.yml
+++ b/.github/workflows/frontend-ci.yml
@@ -40,7 +40,8 @@ jobs:
       - name: Upload coverage reports for lib to Codecov
         uses: codecov/codecov-action@v4
         with:
-          directory: chartlets.js/packages/lib/
+          directory: chartlets.js/packages/lib/coverage/
+          flags: frontend
           verbose: true
           token: ${{ secrets.CODECOV_TOKEN }}