diff --git a/pkg/argocd/git.go b/pkg/argocd/git.go
index 8ec22744..7710b98c 100644
--- a/pkg/argocd/git.go
+++ b/pkg/argocd/git.go
@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"crypto/sha256"
 	"encoding/hex"
+	"errors"
 	"fmt"
 	"os"
 	"path"
@@ -12,6 +13,7 @@ import (
 
 	"sigs.k8s.io/kustomize/api/konfig"
 	"sigs.k8s.io/kustomize/api/types"
+	"sigs.k8s.io/kustomize/kyaml/kio"
 	"sigs.k8s.io/kustomize/kyaml/order"
 	kyaml "sigs.k8s.io/kustomize/kyaml/yaml"
 
@@ -345,43 +347,83 @@ func writeKustomization(app *v1alpha1.Application, wbc *WriteBackConfig, gitC gi
 }
 
 // updateKustomizeFile reads the kustomization file at path, applies the filter to it, and writes the result back
-// to the file. This is the same behavior as kyaml.UpdateFile, but it preserves the original order
-// of YAML fields to minimize git diffs.
+// to the file. This is the same behavior as kyaml.UpdateFile, but it preserves the original order of YAML fields
+// and indentation of YAML sequences to minimize git diffs.
 func updateKustomizeFile(filter kyaml.Filter, path string) (error, bool) {
-	// Read the yaml
-	y, err := kyaml.ReadFile(path)
+	// Open the input file for read
+	yRaw, err := os.ReadFile(path)
 	if err != nil {
 		return err, false
 	}
 
-	originalData, err := y.String()
+	// Read the yaml document from bytes
+	originalYSlice, err := kio.FromBytes(yRaw)
 	if err != nil {
 		return err, false
 	}
 
+	// Check that we are dealing with a single document
+	if len(originalYSlice) != 1 {
+		return errors.New("target parameter file should contain a single YAML document"), false
+	}
+	originalY := originalYSlice[0]
+
+	// Get the (parsed) original document
+	originalData, err := originalY.String()
+	if err != nil {
+		return err, false
+	}
+
+	// Create a reader, preserving indentation of sequences
+	var out bytes.Buffer
+	rw := &kio.ByteReadWriter{
+		Reader:            bytes.NewBuffer(yRaw),
+		Writer:            &out,
+		PreserveSeqIndent: true,
+	}
+
+	// Read from input buffer
+	newYSlice, err := rw.Read()
+	if err != nil {
+		return err, false
+	}
+	// We can safely assume we have a single document from the previous check
+	newY := newYSlice[0]
+
 	// Update the yaml
-	yCpy := y.Copy()
-	if err := yCpy.PipeE(filter); err != nil {
+	if err := newY.PipeE(filter); err != nil {
 		return err, false
 	}
 
 	// Preserve the original order of fields
-	if err := order.SyncOrder(y, yCpy); err != nil {
+	if err := order.SyncOrder(originalY, newY); err != nil {
 		return err, false
 	}
 
-	override, err := yCpy.String()
+	// Write the yaml document to the output buffer
+	if err = rw.Write([]*kyaml.RNode{newY}); err != nil {
+		return err, false
+	}
+
+	// newY contains metadata used by kio to preserve sequence indentation,
+	// hence we need to parse the output buffer instead
+	newParsedY, err := kyaml.Parse(out.String())
+	if err != nil {
+		return err, false
+	}
+	newData, err := newParsedY.String()
 	if err != nil {
 		return err, false
 	}
 
-	if originalData == override {
+	// Compare the updated document with the original document
+	if originalData == newData {
 		log.Debugf("target parameter file and marshaled data are the same, skipping commit.")
 		return nil, true
 	}
 
-	// Write the yaml
-	if err := os.WriteFile(path, []byte(override), 0600); err != nil {
+	// Write to file the changes
+	if err := os.WriteFile(path, out.Bytes(), 0600); err != nil {
 		return err, false
 	}
 
diff --git a/pkg/argocd/git_test.go b/pkg/argocd/git_test.go
index cfd79148..7db7aad5 100644
--- a/pkg/argocd/git_test.go
+++ b/pkg/argocd/git_test.go
@@ -267,6 +267,18 @@ func Test_updateKustomizeFile(t *testing.T) {
 			wantContent: `images:
 - name: foo
   digest: sha23456
+`,
+			filter: filter,
+		},
+		{
+			name: "indented",
+			content: `images:
+  - name: foo
+    digest: sha12345
+`,
+			wantContent: `images:
+  - name: foo
+    digest: sha23456
 `,
 			filter: filter,
 		},