diff --git a/cmd/flux/migrate.go b/cmd/flux/migrate.go
index 01449f14..11c6c3e1 100644
--- a/cmd/flux/migrate.go
+++ b/cmd/flux/migrate.go
@@ -624,18 +624,35 @@ func (f *FileSystemMigrator) detectFileUpgrades(file string) ([]APIUpgrade, erro
 			continue
 		}
 
-		// Parse kind.
-		if line+1 >= len(lines) {
-			continue
-		}
-		kindLine := lines[line+1]
+		// Parse kind. YAML allows fields to be ordered arbitrarily, so the
+		// kind: line may appear before or after apiVersion: within the same
+		// document. Search within the current document boundaries (delimited
+		// by "---" separators) rather than hard-coding line+1.
 		const kindPrefix = "kind: "
-		idx = strings.Index(kindLine, kindPrefix)
-		if idx == -1 {
+		kind := ""
+		for j := line - 1; j >= 0; j-- {
+			if strings.HasPrefix(strings.TrimSpace(lines[j]), "---") {
+				break
+			}
+			if k := strings.Index(lines[j], kindPrefix); k != -1 {
+				kind = strings.Split(strings.TrimSpace(lines[j][k+len(kindPrefix):]), " ")[0]
+				break
+			}
+		}
+		if kind == "" {
+			for j := line + 1; j < len(lines); j++ {
+				if strings.HasPrefix(strings.TrimSpace(lines[j]), "---") {
+					break
+				}
+				if k := strings.Index(lines[j], kindPrefix); k != -1 {
+					kind = strings.Split(strings.TrimSpace(lines[j][k+len(kindPrefix):]), " ")[0]
+					break
+				}
+			}
+		}
+		if kind == "" {
 			continue
 		}
-		kindValuePrefix := strings.TrimSpace(kindLine[idx+len(kindPrefix):])
-		kind := strings.Split(kindValuePrefix, " ")[0]
 
 		// Build GroupKind.
 		gk := schema.GroupKind{
diff --git a/cmd/flux/migrate_test.go b/cmd/flux/migrate_test.go
index 0820fb82..bd16649e 100644
--- a/cmd/flux/migrate_test.go
+++ b/cmd/flux/migrate_test.go
@@ -71,6 +71,17 @@ func TestFileSystemMigrator(t *testing.T) {
 				},
 			},
 		},
+		{
+			name:         "migrate single file with non-adjacent apiVersion and kind",
+			path:         "testdata/migrate/file-system/non-adjacent-kind.yaml",
+			outputGolden: "testdata/migrate/file-system/non-adjacent-kind.yaml.output.golden",
+			writtenFiles: []writtenFile{
+				{
+					file:       "testdata/migrate/file-system/non-adjacent-kind.yaml",
+					goldenFile: "testdata/migrate/file-system/non-adjacent-kind.yaml.golden",
+				},
+			},
+		},
 		{
 			name:         "migrate files in directory",
 			path:         "testdata/migrate/file-system/dir",
diff --git a/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml
new file mode 100644
index 00000000..79aef13a
--- /dev/null
+++ b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml
@@ -0,0 +1,14 @@
+apiVersion: image.toolkit.fluxcd.io/v1beta1
+metadata:
+  name: podinfo
+kind: ImageRepository
+---
+metadata:
+  name: alpine
+kind: ImagePolicy
+apiVersion: image.toolkit.fluxcd.io/v1beta2
+---
+kind: ImageUpdateAutomation
+metadata:
+  name: flux-system
+apiVersion: image.toolkit.fluxcd.io/v1beta1
diff --git a/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.golden b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.golden
new file mode 100644
index 00000000..9e4ea650
--- /dev/null
+++ b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.golden
@@ -0,0 +1,14 @@
+apiVersion: image.toolkit.fluxcd.io/v1
+metadata:
+  name: podinfo
+kind: ImageRepository
+---
+metadata:
+  name: alpine
+kind: ImagePolicy
+apiVersion: image.toolkit.fluxcd.io/v1
+---
+kind: ImageUpdateAutomation
+metadata:
+  name: flux-system
+apiVersion: image.toolkit.fluxcd.io/v1
diff --git a/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.output.golden b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.output.golden
new file mode 100644
index 00000000..da1f34f2
--- /dev/null
+++ b/cmd/flux/testdata/migrate/file-system/non-adjacent-kind.yaml.output.golden
@@ -0,0 +1,6 @@
+► starting migration of custom resources
+✚ testdata/migrate/file-system/non-adjacent-kind.yaml:1: ImageRepository v1beta1 -> v1
+✚ testdata/migrate/file-system/non-adjacent-kind.yaml:9: ImagePolicy v1beta2 -> v1
+✚ testdata/migrate/file-system/non-adjacent-kind.yaml:14: ImageUpdateAutomation v1beta1 -> v1
+✔ file testdata/migrate/file-system/non-adjacent-kind.yaml migrated successfully
+✔ custom resources migrated successfully