diff --git a/bitbake/lib/bb/cooker.py b/bitbake/lib/bb/cooker.py
index 07202e3392..e4cff3a23e 100644
--- a/bitbake/lib/bb/cooker.py
+++ b/bitbake/lib/bb/cooker.py
@@ -334,6 +334,8 @@ class BBCooker:
                         contents[begin_line] = "\n"
                     #remove var from history
                     self.data.varhistory.del_var_history(var, conf_file, line)
+                    #remove variable
+                    self.data.delVar(var)
 
                 with open(conf_file, 'w') as f:
                     f.writelines(contents)