diff --git a/.github/workflows/multiservice-discovery-diff.yaml b/.github/workflows/multiservice-discovery-diff.yaml
index 0b14f72eb..06caf2530 100644
--- a/.github/workflows/multiservice-discovery-diff.yaml
+++ b/.github/workflows/multiservice-discovery-diff.yaml
@@ -10,7 +10,7 @@ on:
 concurrency: 
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
-  
+
 jobs:
   msd-diff:
     runs-on: ubuntu-20.04
@@ -30,18 +30,38 @@ jobs:
           workflow: main.yaml
 
       - name: "🔭 Compute MSD"
+        id: msd-diff
         run: |
           set -exuo pipefail
-          mkdir -p tmp/main-registry tmp/branch-registry main-targets branch-targets
+          REGISTRY_DIR_MAIN="$HOME/tmp/main-registry"
+          REGISTRY_DIR_BRANCH="$HOME/tmp/branch-registry"
+          TARGETS_DIR_MAIN="$HOME/main-targets"
+          TARGETS_DIR_BRANCH="$HOME/branch-targets"
+
+          mkdir -p "$REGISTRY_DIR_MAIN" \
+                  "$REGISTRY_DIR_BRANCH" \
+                  "$TARGETS_DIR_MAIN" \
+                  "$TARGETS_DIR_BRANCH"
           chmod +x multiservice-discovery
-          ./multiservice-discovery --targets-dir tmp/main-registry --render-prom-targets-to-stdout > main-targets/targets.json
-          bazel run //rs/ic-observability/multiservice-discovery -- --targets-dir $(pwd)/tmp/branch-registry --render-prom-targets-to-stdout > branch-targets/targets.json
+
+          # Run multiservice-discovery for main targets
+          ./multiservice-discovery \
+              --targets-dir "$REGISTRY_DIR_MAIN" \
+              --render-prom-targets-to-stdout > "$TARGETS_DIR_MAIN/targets.json"
+
+          # Run multiservice-discovery for branch targets with bazel
+          bazel run //rs/ic-observability/multiservice-discovery -- \
+              --targets-dir "$REGISTRY_DIR_BRANCH" \
+              --render-prom-targets-to-stdout > "$TARGETS_DIR_BRANCH/targets.json"
+
+          echo "targets_main=$TARGETS_DIR_MAIN" >> $GITHUB_OUTPUT
+          echo "targets_branch=$TARGETS_DIR_BRANCH" >> $GITHUB_OUTPUT
 
       - name: "Check MSD Diff"
         uses: "int128/diff-action@v1"
         with:
-          base: /home/runner/work/dre/dre/main-targets
-          head: /home/runner/work/dre/dre/branch-targets
+          base: ${{ steps.msd-diff.outputs.targets_main }}
+          head: ${{ steps.msd-diff.outputs.targets_branch }}
           comment-header: |
             ## MSD Diff
             Remove `prevent-merging-MSD-diff` label to merge after inspection