diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index c6c7975..b30af18 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -48,6 +48,9 @@ for entry in "${GENOMES[@]}"; do
         # Initial genome push
         git add .
         git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
+
+        git branch -M main
+
         git push -u origin main
 
         # Key export and instructions
diff --git a/scripts/setup-master.sh b/scripts/setup-master.sh
index 181c01e..66fe82a 100644
--- a/scripts/setup-master.sh
+++ b/scripts/setup-master.sh
@@ -37,5 +37,7 @@ scaffold_master "."
 git add .
 git commit -m "chore: initialize master scaffold" || info "No changes to commit in master."
 
+git branch -M main
+
 # 3. Initial Push
 git push -u origin main