diff --git a/pkg/config/app_config.go b/pkg/config/app_config.go
index 936dcb64a..d68620867 100644
--- a/pkg/config/app_config.go
+++ b/pkg/config/app_config.go
@@ -196,10 +196,14 @@ func loadUserConfig(configFiles []*ConfigFile, base *UserConfig) (*UserConfig, e
 			return nil, err
 		}
 
+		existingCustomCommands := base.CustomCommands
+
 		if err := yaml.Unmarshal(content, base); err != nil {
 			return nil, fmt.Errorf("The config at `%s` couldn't be parsed, please inspect it before opening up an issue.\n%w", path, err)
 		}
 
+		base.CustomCommands = append(base.CustomCommands, existingCustomCommands...)
+
 		if err := base.Validate(); err != nil {
 			return nil, fmt.Errorf("The config at `%s` has a validation error.\n%w", path, err)
 		}
diff --git a/pkg/integration/tests/config/custom_commands_in_per_repo_config.go b/pkg/integration/tests/config/custom_commands_in_per_repo_config.go
index 4cff322ef..81f8724aa 100644
--- a/pkg/integration/tests/config/custom_commands_in_per_repo_config.go
+++ b/pkg/integration/tests/config/custom_commands_in_per_repo_config.go
@@ -49,10 +49,7 @@ customCommands:
 		t.Views().Status().Content(Contains("other → master"))
 
 		t.GlobalPress("X")
-		/* EXPECTED:
 		t.FileSystem().FileContent("../other/file.txt", Equals("global X"))
-		ACTUAL: */
-		t.FileSystem().PathNotPresent("../other/file.txt")
 
 		t.GlobalPress("Y")
 		t.FileSystem().FileContent("../other/file.txt", Equals("local Y"))