diff --git a/pkg/app/entry_point.go b/pkg/app/entry_point.go
index 96f6176c7..d23519a98 100644
--- a/pkg/app/entry_point.go
+++ b/pkg/app/entry_point.go
@@ -136,6 +136,12 @@ func Start(buildInfo *BuildInfo, integrationTest integrationTypes.IntegrationTes
 
 	if integrationTest != nil {
 		integrationTest.SetupConfig(appConfig)
+
+		// Preserve the changes that the test setup just made to the config, so
+		// they don't get lost when we reload the config while running the test
+		// (which happens when switching between repos, going in and out of
+		// submodules, etc).
+		appConfig.SaveGlobalUserConfig()
 	}
 
 	common, err := NewCommon(appConfig)
diff --git a/pkg/config/app_config.go b/pkg/config/app_config.go
index 3460c4b00..e30ff4a26 100644
--- a/pkg/config/app_config.go
+++ b/pkg/config/app_config.go
@@ -2,6 +2,7 @@ package config
 
 import (
 	"fmt"
+	"log"
 	"os"
 	"path/filepath"
 	"strings"
@@ -361,6 +362,24 @@ func loadAppState() (*AppState, error) {
 	return appState, nil
 }
 
+// SaveGlobalUserConfig saves the UserConfig back to disk. This is only used in
+// integration tests, so we are a bit sloppy with error handling.
+func (c *AppConfig) SaveGlobalUserConfig() {
+	if len(c.userConfigFiles) != 1 {
+		panic("expected exactly one global user config file")
+	}
+
+	yamlContent, err := yaml.Marshal(c.userConfig)
+	if err != nil {
+		log.Fatalf("error marshalling user config: %v", err)
+	}
+
+	err = os.WriteFile(c.userConfigFiles[0].Path, yamlContent, 0o644)
+	if err != nil {
+		log.Fatalf("error saving user config: %v", err)
+	}
+}
+
 // AppState stores data between runs of the app like when the last update check
 // was performed and which other repos have been checked out
 type AppState struct {