diff --git a/augur/application/cli/backend.py b/augur/application/cli/backend.py
index 46761084a6..84c91eaf03 100644
--- a/augur/application/cli/backend.py
+++ b/augur/application/cli/backend.py
@@ -13,6 +13,7 @@
 import uuid
 import traceback
 import requests
+import tempfile
 from redis.exceptions import ConnectionError as RedisConnectionError
 
 from augur.tasks.start_tasks import augur_collection_monitor, create_collection_status_records
@@ -23,6 +24,8 @@
 from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model
 from augur.application.db.models import UserRepo
 from augur.application.db.session import DatabaseSession
+from augur.application.config import AugurConfig
+from augur.application.db import get_engine
 from augur.application.logs import AugurLogger
 from augur.application.service_manager import AugurServiceManager, cleanup_collection_status_and_rabbit, clean_collection_status
 from augur.application.db.lib import get_value
@@ -35,6 +38,48 @@
 
 logger = AugurLogger("augur", reset_logfiles=reset_logs).get_logger()
 
+def create_git_credential_file(github_key, gitlab_key):
+    if 'AUGUR_GITHUB_USERNAME' in os.environ:
+        print("Found AUGUR_GITHUB_USERNAME env variable")
+        github_username = os.environ.get("AUGUR_GITHUB_USERNAME")
+    else:
+        github_username = input("Please input your GitHub username")
+    
+    if 'AUGUR_GITLAB_USERNAME' in os.environ:
+        print("Found AUGUR_GITLAB_USERNAME env variable")
+        gitlab_username = os.environ.get("AUGUR_GITLAB_USERNAME")
+    else:
+        gitlab_username = input("Please input your GitLab username")
+    
+
+    engine = get_engine()
+    with DatabaseSession(logger, engine) as session:
+        config = AugurConfig(logger, session)
+    
+        worker_options = config.get_section("Facade")
+        repo_base_directory = worker_options['repo_directory']
+    
+    credential_file_text = f"""
+        https://{github_username}:{github_key}@github.com
+        https://{gitlab_username}:{gitlab_key}@gitlab.com
+    """
+
+    link_path = f"{repo_base_directory}/.git-credentials"
+    fd, temp_path = tempfile.mkstemp(prefix="myapp_", suffix=".tmp")
+    with os.fdopen(fd, "w") as f:
+        f.write(credential_file_text)
+    
+    # Create a temporary symlink
+    tmp_link = link_path + ".new"
+    os.symlink(temp_path, tmp_link)
+    # Atomically swap it into place
+    os.replace(tmp_link, link_path)
+
+    facade_credential_store = f"git config --global credential.helper \"store --file {repo_base_directory}/.git-credentials\""
+    subprocess.Popen(facade_credential_store.split(" "))
+    
+
+
 @click.group('server', short_help='Commands for controlling the backend API server & data collection workers')
 @click.pass_context
 def cli(ctx):
@@ -168,7 +213,10 @@ def start(ctx, disable_collection, development, pidfile, port):
 
             clean_collection_status(session)
             assign_orphan_repos_to_default_user(session)
-        
+
+        #Create git credentials file and store git credentials
+        create_git_credential_file(ghkeyman.keys[0], glkeyman.keys[0])
+
         create_collection_status_records.si().apply_async()
         time.sleep(3)
 
diff --git a/scripts/install/config.sh b/scripts/install/config.sh
index 0408b0aa09..c634366d4f 100755
--- a/scripts/install/config.sh
+++ b/scripts/install/config.sh
@@ -226,13 +226,13 @@ function create_config() {
     fi
 
     #Create and cache credentials for github and gitlab
-    touch $facade_repo_directory/.git-credentials
+    #touch $facade_repo_directory/.git-credentials
 
-    echo "https://$github_username:$github_api_key@github.com" > $facade_repo_directory/.git-credentials
-    echo "https://$gitlab_username:$gitlab_api_key@gitlab.com" >> $facade_repo_directory/.git-credentials
+    #echo "https://$github_username:$github_api_key@github.com" > $facade_repo_directory/.git-credentials
+    #echo "https://$gitlab_username:$gitlab_api_key@gitlab.com" >> $facade_repo_directory/.git-credentials
 
-    git config --global credential.helper "store --file $facade_repo_directory/.git-credentials"
-    "${cmd[@]}"
+    #git config --global credential.helper "store --file $facade_repo_directory/.git-credentials"
+    #"${cmd[@]}"
 }
 echo
 echo "Collecting data for config..."