diff --git a/kolibri/utils/options.py b/kolibri/utils/options.py
index 8a3005e196c..b990691955d 100644
--- a/kolibri/utils/options.py
+++ b/kolibri/utils/options.py
@@ -992,6 +992,12 @@ def generate_empty_options_file(ini_filename="options.ini"):
 
     conf = read_options_file(ini_filename=ini_filename)
 
+    for section, opts in option_spec.items():
+        for optname, attrs in opts.items():
+            for envvar in attrs.get("envvars", []):
+                if envvar in os.environ:
+                    conf[section].pop(optname, None)
+
     comments = None
 
     for section, opts in option_spec.items():