diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
index 25bb924922..2a00f15f41 100644
--- a/.github/workflows/deploy_docs.yml
+++ b/.github/workflows/deploy_docs.yml
@@ -20,7 +20,7 @@ jobs:
   build-jekyll:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout gh-pages
+      - name: Checkout
         uses: actions/checkout@v4
         with:
           ref: gh-pages
@@ -57,26 +57,37 @@ jobs:
       - name: Generate Doxygen Documentation
         run: |
           branches=("master:core" "duo" "handle" "orbit" "gloves" "desktop" "spark" "chromadeck")
+          rm -rf docs || true
+          mkdir -p docs # Ensure the docs directory is clean and prepared
 
           for item in "${branches[@]}"; do
             IFS=':' read -r branch dest <<< "$item"
             dest="${dest:-$branch}"
 
-            # Ensure the output directory exists
-            mkdir -p docs/$dest
+            # Create a worktree for the branch in a separate directory
+            echo "Setting up worktree for branch: $branch"
+            git worktree add worktree/$branch $branch
+
+            # Change directory to the worktree
+            cd worktree/$branch
 
-            # Checkout each branch and generate documentation
-            echo "Checking out branch: $branch"
-            git checkout $branch
+            # Ensure the output directory exists
+            mkdir -p ../../docs/$dest
 
             # Change OUTPUT_DIRECTORY in Doxyfile for each branch
             echo "Adjusting Doxyfile for branch: $branch"
-            sed -i "s|OUTPUT_DIRECTORY *=.*|OUTPUT_DIRECTORY = docs/$dest|" Doxyfile
+            sed -i "s|OUTPUT_DIRECTORY *=.*|OUTPUT_DIRECTORY = ../../docs/$dest|" Doxyfile
 
             echo "Running Doxygen for branch: $branch"
             doxygen Doxyfile || { echo "Doxygen failed for branch: $branch"; exit 1; }
 
             echo "Generated docs for $branch in docs/$dest"
+
+            # Return to the root directory
+            cd ../..
+
+            # Remove the worktree after processing
+            git worktree remove worktree/$branch -f
           done
 
       - name: Upload Doxygen Docs