diff --git a/core/pkg/fixhandler/fixhandler.go b/core/pkg/fixhandler/fixhandler.go
index 399e2aac..dbe1e049 100644
--- a/core/pkg/fixhandler/fixhandler.go
+++ b/core/pkg/fixhandler/fixhandler.go
@@ -208,8 +208,6 @@ func (h *FixHandler) ApplyChanges(ctx context.Context, resourcesToFix []Resource
 			continue
 		}
 
-		fileAsString = sanitizeYaml(fileAsString)
-
 		fixedYamlString, err := ApplyFixToContent(ctx, fileAsString, yamlExpression)
 
 		if err != nil {
@@ -219,8 +217,6 @@ func (h *FixHandler) ApplyChanges(ctx context.Context, resourcesToFix []Resource
 			updatedFiles[filepath] = true
 		}
 
-		fixedYamlString = revertSanitizeYaml(fixedYamlString)
-
 		err = writeFixesToFile(filepath, fixedYamlString)
 
 		if err != nil {
@@ -247,6 +243,7 @@ func (h *FixHandler) getFilePathAndIndex(filePathWithIndex string) (filePath str
 }
 
 func ApplyFixToContent(ctx context.Context, yamlAsString, yamlExpression string) (fixedString string, err error) {
+	yamlAsString = sanitizeYaml(yamlAsString)
 	newline := determineNewlineSeparator(yamlAsString)
 
 	yamlLines := strings.Split(yamlAsString, newline)
@@ -268,6 +265,7 @@ func ApplyFixToContent(ctx context.Context, yamlAsString, yamlExpression string)
 	fixedYamlLines := getFixedYamlLines(yamlLines, fixInfo, newline)
 
 	fixedString = getStringFromSlice(fixedYamlLines, newline)
+	fixedString = revertSanitizeYaml(fixedString)
 
 	return fixedString, nil
 }
diff --git a/core/pkg/fixhandler/fixhandler_test.go b/core/pkg/fixhandler/fixhandler_test.go
index 5df11774..a372451b 100644
--- a/core/pkg/fixhandler/fixhandler_test.go
+++ b/core/pkg/fixhandler/fixhandler_test.go
@@ -169,6 +169,12 @@ func getTestCases() []indentationTestCase {
 			 select(di==0).spec.securityContext.runAsRoot |= false`,
 			"hybrids/tc-04-01-expected.yaml",
 		},
+		{
+			"hybrids/tc-05-00-input-leading-doc-separator.yaml",
+			`del(select(di==0).spec.containers[0].securityContext) |
+			 select(di==0).spec.securityContext.runAsRoot |= false`,
+			"hybrids/tc-05-01-expected.yaml",
+		},
 	}
 
 	return indentationTestCases
@@ -196,9 +202,8 @@ func TestApplyFixKeepsFormatting(t *testing.T) {
 			want := string(wantRaw)
 			expression := tc.yamlExpression
 
-			fileAsString := sanitizeYaml(string(input))
-			fixedYamlString, _ := ApplyFixToContent(context.TODO(), fileAsString, expression)
-			got := revertSanitizeYaml(fixedYamlString)
+			fileAsString := string(input)
+			got, _ := ApplyFixToContent(context.TODO(), fileAsString, expression)
 
 			assert.Equalf(
 				t, want, got,
@@ -288,9 +293,8 @@ func Test_sanitizeYaml(t *testing.T) {
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			if got := sanitizeYaml(tt.args.fileAsString); got != tt.want {
-				t.Errorf("sanitizeYaml() = %v, want %v", got, tt.want)
-			}
+			got := sanitizeYaml(tt.args.fileAsString)
+			assert.Equal(t, tt.want, got)
 		})
 	}
 }
@@ -321,9 +325,8 @@ func Test_revertSanitizeYaml(t *testing.T) {
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			if got := revertSanitizeYaml(tt.args.fixedYamlString); got != tt.want {
-				t.Errorf("revertSanitizeYaml() = %v, want %v", got, tt.want)
-			}
+			got := revertSanitizeYaml(tt.args.fixedYamlString)
+			assert.Equal(t, tt.want, got)
 		})
 	}
 }
diff --git a/core/pkg/fixhandler/testdata/hybrids/tc-05-00-input-leading-doc-separator.yaml b/core/pkg/fixhandler/testdata/hybrids/tc-05-00-input-leading-doc-separator.yaml
new file mode 100644
index 00000000..9a6bc1bf
--- /dev/null
+++ b/core/pkg/fixhandler/testdata/hybrids/tc-05-00-input-leading-doc-separator.yaml
@@ -0,0 +1,22 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+---
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+
+      image: nginx
+
+      securityContext:
+        runAsRoot: true
diff --git a/core/pkg/fixhandler/testdata/hybrids/tc-05-01-expected.yaml b/core/pkg/fixhandler/testdata/hybrids/tc-05-01-expected.yaml
new file mode 100644
index 00000000..5beb28d4
--- /dev/null
+++ b/core/pkg/fixhandler/testdata/hybrids/tc-05-01-expected.yaml
@@ -0,0 +1,22 @@
+# Fix to Apply:
+# REMOVE:
+# "del(select(di==0).spec.containers[0].securityContext)"
+
+# INSERT:
+# select(di==0).spec.securityContext.runAsRoot: false
+
+
+---
+apiVersion: v1
+kind: Pod
+metadata:
+  name: insert_to_mapping_node_1
+
+spec:
+  containers:
+    - name: nginx_container
+
+      image: nginx
+  securityContext:
+    runAsRoot: false
+