diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 777f51d..c5c3999 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -49,12 +49,14 @@ for entry in "${GENOMES[@]}"; do
         git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
         git push -u origin main
 
-        # Key export and instructions (Fix Obs B)
+        # Key export and instructions
         gcrypt_export_key "${GENOME_NAME}"
         gcrypt_print_key_instructions "${GENOME_NAME}"
 
-        # Return to master to consolidate the submodule addition
+        # Commit the submodule reference in the master repo
         cd "${WORK_DIR}/${MASTER_REPO}"
+        git commit -m "feat: add ${GENOME_NAME} as submodule"
+        git push origin main
     fi
 done