diff --git a/.github/workflows/make_prs_for_other_repos.yaml b/.github/workflows/make_prs_for_other_repos.yaml
index d44aa00e8..c8fc863d4 100644
--- a/.github/workflows/make_prs_for_other_repos.yaml
+++ b/.github/workflows/make_prs_for_other_repos.yaml
@@ -13,14 +13,20 @@ jobs:
       DESTINATION_REPO_DIR: nextstrain.org
 
     steps:
-      - name: Generate Markdown link
-        id: generate-markdown-link
+      # If a PR exists for this branch, set the Auspice SHA for npm install to
+      # the GitHub-managed merge ref. Otherwise, just use the GITHUB_SHA from
+      # workflow_dispatch which represents the branch HEAD.
+      - name: Detect PR from branch
+        id: detect-pr
         run: |
           PR_NUMBER=$(gh pr view $GITHUB_REF_NAME --repo nextstrain/auspice --json 'number' --jq '.number') || true
           if [[ -n $PR_NUMBER ]]; then
-            echo "::set-output name=text::[PR $PR_NUMBER](https://github.com/nextstrain/auspice/pull/$PR_NUMBER)"
+            echo "::set-output name=markdown-text::[PR $PR_NUMBER](https://github.com/nextstrain/auspice/pull/$PR_NUMBER)"
+            MERGE_SHA=$(gh pr view $GITHUB_REF_NAME --repo nextstrain/auspice --json 'potentialMergeCommit' --jq '.potentialMergeCommit.oid')
+            echo "::set-output name=auspice-sha::$MERGE_SHA"
           else
-            echo "::set-output name=text::[branch $GITHUB_REF_NAME](https://github.com/nextstrain/auspice/tree/$GITHUB_REF_NAME)"
+            echo "::set-output name=markdown-text::[branch $GITHUB_REF_NAME](https://github.com/nextstrain/auspice/tree/$GITHUB_REF_NAME)"
+            echo "::set-output name=auspice-sha::$GITHUB_SHA"
           fi
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -35,12 +41,12 @@ jobs:
           repository: nextstrain/nextstrain.org
           path: ${{ env.DESTINATION_REPO_DIR }}
 
-      - name: Install Auspice from source branch HEAD commit
+      - name: Install Auspice
         shell: bash
         working-directory: ${{ env.DESTINATION_REPO_DIR }}
         run: |
           npm ci
-          npm install nextstrain/auspice#${GITHUB_SHA}
+          npm install nextstrain/auspice#${{ steps.detect-pr.outputs.auspice-sha }}
           git add package.json package-lock.json
 
       - name: Create Pull Request for testing on nextstrain.org repo
@@ -55,9 +61,12 @@ jobs:
           committer: 'nextstrain-bot <nextstrain-bot@users.noreply.github.com>'
           title: '[bot] [DO NOT MERGE] Test Auspice branch ${{ github.ref_name }}'
           body: |
-            This PR has been created to test Auspice from ${{ steps.generate-markdown-link.outputs.text }}.
+            This PR has been created to test Auspice from ${{ steps.detect-pr.outputs.markdown-text }}.
 
             This message and corresponding commits were automatically created by a GitHub Action from [nextstrain/auspice](https://github.com/nextstrain/auspice).
+
+            If there is an open PR for the branch, then Auspice has been installed from the result of the branch merged with the PR's target branch.
+            This will surface any issues that can arise from merging the PR in Auspice. To address these issues locally, update the source branch (e.g. with a git rebase).
           draft: true
           delete-branch: true