diff --git a/cmd/flux/migrate.go b/cmd/flux/migrate.go
index 3a0129ce..7beba3c7 100644
--- a/cmd/flux/migrate.go
+++ b/cmd/flux/migrate.go
@@ -157,7 +157,7 @@ The command has two modes of operation:
   # Simulate the migration without making any changes.
   flux migrate -f . --dry-run
 
-  # Run the migration by skipping confirmation prompts.
+  # Run the migration skipping confirmation prompts.
   flux migrate -f . --yes
 `,
 	RunE: runMigrateCmd,
@@ -177,7 +177,7 @@ func init() {
 	migrateCmd.Flags().StringVarP(&migrateFlags.path, "path", "f", "",
 		"the path to the directory containing the manifests to migrate")
 	migrateCmd.Flags().StringSliceVarP(&migrateFlags.extensions, "extensions", "e", []string{".yaml", ".yml"},
-		"the file extensions to consider when migrating manifests, only applicable --path")
+		"the file extensions to consider when migrating manifests, only applicable with --path")
 	migrateCmd.Flags().StringVarP(&migrateFlags.version, "version", "v", "",
 		"the target Flux minor version to migrate manifests to, only applicable with --path (defaults to the version of the CLI)")
 	migrateCmd.Flags().BoolVarP(&migrateFlags.yes, "yes", "y", false,
@@ -605,7 +605,8 @@ func (f *FileSystemMigrator) detectFileUpgrades(file string) ([]APIUpgrade, erro
 		if idx == -1 {
 			continue
 		}
-		apiVersion := strings.TrimSpace(apiVersionLine[idx+len(apiVersionPrefix):])
+		apiVersionValuePrefix := strings.TrimSpace(apiVersionLine[idx+len(apiVersionPrefix):])
+		apiVersion := strings.Split(apiVersionValuePrefix, " ")[0]
 		gv, err := schema.ParseGroupVersion(apiVersion)
 		if err != nil {
 			logger.Warningf("%s:%d: %v", file, line+1, err)
@@ -669,7 +670,7 @@ func (f *FileSystemMigrator) migrateFile(fileUpgrades *FileAPIUpgrades) error {
 	// Apply upgrades to lines.
 	for _, upgrade := range fileUpgrades.Upgrades {
 		line := lines[upgrade.Line]
-		line = strings.ReplaceAll(line, upgrade.OldVersion, upgrade.NewVersion)
+		line = strings.Replace(line, upgrade.OldVersion, upgrade.NewVersion, 1)
 		lines[upgrade.Line] = line
 	}
 
diff --git a/cmd/flux/testdata/migrate/file-system/dir.golden/some-file.yaml b/cmd/flux/testdata/migrate/file-system/dir.golden/some-file.yaml
index 011a7ffe..8b8ed51b 100644
--- a/cmd/flux/testdata/migrate/file-system/dir.golden/some-file.yaml
+++ b/cmd/flux/testdata/migrate/file-system/dir.golden/some-file.yaml
@@ -7,6 +7,13 @@ kind: ImageRepository
 apiVersion: image.toolkit.fluxcd.io/v1
 kind: ImagePolicy
 
+---
+spec:
+  wait: true
+  dependsOn:
+    - apiVersion: image.toolkit.fluxcd.io/v1 # update this from v1beta1
+      kind: ImageRepository
+
 
 ---
 
diff --git a/cmd/flux/testdata/migrate/file-system/dir.output.golden b/cmd/flux/testdata/migrate/file-system/dir.output.golden
index ecd7885b..ab536652 100644
--- a/cmd/flux/testdata/migrate/file-system/dir.output.golden
+++ b/cmd/flux/testdata/migrate/file-system/dir.output.golden
@@ -3,9 +3,10 @@
 ⚠️ skipping irregular file testdata/migrate/file-system/dir/some-file-link.yaml
 ✚ testdata/migrate/file-system/dir/some-dir/another-file.yaml:2: ImageUpdateAutomation v1beta2 -> v1
 ✚ testdata/migrate/file-system/dir/some-dir/another-file.yml:3: ImageUpdateAutomation v1beta2 -> v1
-⚠️ testdata/migrate/file-system/dir/some-file.yaml:13: unexpected GroupVersion string: image.toolkit.fluxcd.io/v1/v2
+⚠️ testdata/migrate/file-system/dir/some-file.yaml:20: unexpected GroupVersion string: image.toolkit.fluxcd.io/v1/v2
 ✚ testdata/migrate/file-system/dir/some-file.yaml:1: ImageRepository v1beta1 -> v1
 ✚ testdata/migrate/file-system/dir/some-file.yaml:7: ImagePolicy v1beta2 -> v1
+✚ testdata/migrate/file-system/dir/some-file.yaml:14: ImageRepository v1beta1 -> v1
 ⚠️ testdata/migrate/file-system/dir/some-file.yml:15: unexpected GroupVersion string: image.toolkit.fluxcd.io/v1/v2
 ✚ testdata/migrate/file-system/dir/some-file.yml:3: ImageRepository v1beta2 -> v1
 ✚ testdata/migrate/file-system/dir/some-file.yml:9: ImagePolicy v1beta1 -> v1
diff --git a/cmd/flux/testdata/migrate/file-system/dir/some-file.yaml b/cmd/flux/testdata/migrate/file-system/dir/some-file.yaml
index 3dc8c492..a8b2be01 100644
--- a/cmd/flux/testdata/migrate/file-system/dir/some-file.yaml
+++ b/cmd/flux/testdata/migrate/file-system/dir/some-file.yaml
@@ -7,6 +7,13 @@ kind: ImageRepository
 apiVersion: image.toolkit.fluxcd.io/v1beta2
 kind: ImagePolicy
 
+---
+spec:
+  wait: true
+  dependsOn:
+    - apiVersion: image.toolkit.fluxcd.io/v1beta1 # update this from v1beta1
+      kind: ImageRepository
+
 
 ---