diff --git a/agentstack/generation/files.py b/agentstack/generation/files.py
index 4400dc34..4aaab327 100644
--- a/agentstack/generation/files.py
+++ b/agentstack/generation/files.py
@@ -123,7 +123,11 @@ def parse_line(line):
     def write(self):
         with open(self._path / self._filename, 'a') as f:
             for key, value in self._new_variables.items():
-                f.write(f"\n{key}={value}")
+                """
+                We don't want to override values the user may already have set
+                in their environment variables so we add a new line commented out.
+                """
+                f.write(f"\n# {key}={value}")
 
     def __enter__(self) -> 'EnvFile':
         return self
diff --git a/agentstack/templates/crewai/{{cookiecutter.project_metadata.project_slug}}/src/main.py b/agentstack/templates/crewai/{{cookiecutter.project_metadata.project_slug}}/src/main.py
index bba6c84f..22db1322 100644
--- a/agentstack/templates/crewai/{{cookiecutter.project_metadata.project_slug}}/src/main.py
+++ b/agentstack/templates/crewai/{{cookiecutter.project_metadata.project_slug}}/src/main.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
+from dotenv import load_dotenv
+load_dotenv(override=True)
 import sys
 from crew import {{cookiecutter.project_metadata.project_name|replace('-', '')|replace('_', '')|capitalize}}Crew
 import agentops
-from dotenv import load_dotenv
-load_dotenv()
 
 agentops.init(default_tags=['crewai', 'agentstack'])