diff --git a/.github/workflows/update-subtree.yml b/.github/workflows/update-subtree.yml
index 58c43667e9028..939c3b6929de1 100644
--- a/.github/workflows/update-subtree.yml
+++ b/.github/workflows/update-subtree.yml
@@ -85,6 +85,7 @@ jobs:
       if: ${{ env.SUBTREE_PR_EXISTS == 'no' }}
       run: |
         cd splitsh-lite
+        sudo apt-get update
         sudo apt-get install -y golang libgit2-dev
         # git2go upstream hasn't been updated to more recent versions of
         # libgit2, so using a fork that does stay up to date
@@ -110,6 +111,10 @@ jobs:
         fi
 
         git checkout ${NEXT_COMMIT_HASH}
+        # Collect submodule commits; note that submodules (intentionally!)
+        # aren't initialized, hence lines will be prefixed with "-" (see git
+        # submodule --help).
+        git submodule status  -- library/ | sed 's/^-//' > ../submodule-heads
         /usr/bin/time -v ../splitsh-lite/splitsh-lite --progress --prefix=library --target subtree/library
         git checkout -b subtree/library subtree/library
 
@@ -165,6 +170,7 @@ jobs:
           fi
         fi
         git checkout main
+        git submodule foreach 'git fetch'
 
         # Tell git about the correct merge base to use, which is the subtree
         # head that we last merged from.
@@ -178,6 +184,8 @@ jobs:
             -c user.name=gitbot -c user.email=git@bot \
             merge -Xsubtree=library subtree/library; then
           echo "MERGE_CONFLICTS=yes" >> $GITHUB_ENV
+          # Ignore submodule conflicts, those are dealt with below.
+          for d in $(cat ../submodule-heads | cut -f2 -d" ") ; do git reset HEAD $d ; done
           git -c user.name=gitbot -c user.email=git@bot commit -a -m "Merge from $NEXT_COMMIT_HASH with conflicts"
         else
           echo "MERGE_CONFLICTS=no" >> $GITHUB_ENV
@@ -187,6 +195,12 @@ jobs:
         NEW_SUBTREE_HEAD=$(git rev-parse subtree/library)
         echo "NEW_SUBTREE_HEAD=${NEW_SUBTREE_HEAD}" >> $GITHUB_ENV
 
+        # Set submodules to upstream versions
+        git submodule update --init
+        git submodule foreach 'grep $sm_path $toplevel/../submodule-heads | cut -f1 -d" " | xargs git checkout'
+        git -c user.name=gitbot -c user.email=git@bot \
+          commit -m "Update submodules" library/
+
         sed -i "s/^channel = \"nightly-.*\"/channel = \"nightly-${NEXT_TOOLCHAIN_DATE}\"/" rust-toolchain.toml
         git -c user.name=gitbot -c user.email=git@bot \
           commit -m "Update toolchain to ${NEXT_TOOLCHAIN_DATE}" rust-toolchain.toml