diff --git a/pkg/migrate/migrator_v1_v1fast.go b/pkg/migrate/migrator_v1_v1fast.go
index 564663551d..3422a6def8 100644
--- a/pkg/migrate/migrator_v1_v1fast.go
+++ b/pkg/migrate/migrator_v1_v1fast.go
@@ -240,7 +240,13 @@ func (g *MigratorV1ToV1Fast) flushConfig(cfg *config.Config, dir string, configF
 	}
 	defer file.Close()
 	console.Infof("Writing config changes to %s.", configFilepath)
-	_, err = file.WriteString(configStr)
+
+	mergedCfgData, err := OverwrightYAML(data, content)
+	if err != nil {
+		return err
+	}
+
+	_, err = file.WriteString(string(mergedCfgData))
 	if err != nil {
 		return util.WrapError(err, "Failed to write config changes")
 	}
diff --git a/pkg/migrate/migrator_v1_v1fast_test.go b/pkg/migrate/migrator_v1_v1fast_test.go
index 691f2dcb73..6e1f6ee685 100644
--- a/pkg/migrate/migrator_v1_v1fast_test.go
+++ b/pkg/migrate/migrator_v1_v1fast_test.go
@@ -66,10 +66,10 @@ class Predictor(BasePredictor):
 	content, err := io.ReadAll(file)
 	require.NoError(t, err)
 	require.Equal(t, `build:
-  python_version: "3.11"
-  python_requirements: requirements.txt
-  fast: true
-predict: predict.py:Predictor
+    python_version: "3.11"
+    python_requirements: requirements.txt
+    fast: true
+predict: "predict.py:Predictor"
 `, string(content))
 	err = file.Close()
 	require.NoError(t, err)
@@ -155,11 +155,78 @@ class Predictor(BasePredictor):
 	content, err := io.ReadAll(file)
 	require.NoError(t, err)
 	require.Equal(t, `build:
-  gpu: true
+    gpu: true
+    python_version: "3.11"
+    python_requirements: requirements.txt
+    fast: true
+predict: "predict.py:Predictor"
+`, string(content))
+	err = file.Close()
+	require.NoError(t, err)
+}
+
+func TestMigrateYAMLComments(t *testing.T) {
+	// Set our new working directory to a temp directory
+	originalDir, err := os.Getwd()
+	require.NoError(t, err)
+	defer func() {
+		err := os.Chdir(originalDir)
+		require.NoError(t, err)
+	}()
+	dir := t.TempDir()
+	err = os.Chdir(dir)
+	require.NoError(t, err)
+
+	// Write our test configs/code
+	configFilepath := filepath.Join(dir, "cog.yaml")
+	file, err := os.Create(configFilepath)
+	require.NoError(t, err)
+	_, err = file.WriteString(`# Here we have a YAML comment
+build:
   python_version: "3.11"
-  python_requirements: requirements.txt
   fast: true
-predict: predict.py:Predictor
+  python_packages:
+    - "pillow"
+  run:
+    - command: curl -o /usr/local/bin/pget -L \"https://github.com/replicate/pget/releases/latest/download/pget_$(uname -s)_$(uname -m)\" && chmod +x /usr/local/bin/pget
+  gpu: true
+predict: "predict.py:Predictor"
+`)
+	require.NoError(t, err)
+	err = file.Close()
+	require.NoError(t, err)
+	pythonFilepath := filepath.Join(dir, "predict.py")
+	file, err = os.Create(pythonFilepath)
+	require.NoError(t, err)
+	_, err = file.WriteString(`from cog import BasePredictor, Input
+
+
+class Predictor(BasePredictor):
+    def predict(self, s: str = Input(description="My Input Description", default=None)) -> str:
+        return "hello " + s
+`)
+	require.NoError(t, err)
+	err = file.Close()
+	require.NoError(t, err)
+
+	// Perform the migration
+	logCtx := coglog.NewMigrateLogContext(true)
+	migrator := NewMigratorV1ToV1Fast(false, logCtx)
+	err = migrator.Migrate(t.Context(), "cog.yaml")
+	require.NoError(t, err)
+
+	// Check config output
+	file, err = os.Open(configFilepath)
+	require.NoError(t, err)
+	content, err := io.ReadAll(file)
+	require.NoError(t, err)
+	require.Equal(t, `# Here we have a YAML comment
+build:
+    gpu: true
+    python_version: "3.11"
+    python_requirements: requirements.txt
+    fast: true
+predict: "predict.py:Predictor"
 `, string(content))
 	err = file.Close()
 	require.NoError(t, err)
diff --git a/pkg/migrate/overwrite_yaml.go b/pkg/migrate/overwrite_yaml.go
new file mode 100644
index 0000000000..7e7a1a89b2
--- /dev/null
+++ b/pkg/migrate/overwrite_yaml.go
@@ -0,0 +1,130 @@
+package migrate
+
+import (
+	"fmt"
+
+	"gopkg.in/yaml.v3"
+)
+
+func OverwrightYAML(sourceYaml []byte, destinationYaml []byte) ([]byte, error) {
+	var sourceNode yaml.Node
+	err := yaml.Unmarshal(sourceYaml, &sourceNode)
+	if err != nil {
+		return nil, err
+	}
+
+	var destinationNode yaml.Node
+	err = yaml.Unmarshal(destinationYaml, &destinationNode)
+	if err != nil {
+		return nil, err
+	}
+
+	err = traverseAndCompare(sourceNode.Content[0], destinationNode.Content[0], "")
+	if err != nil {
+		return nil, err
+	}
+
+	return yaml.Marshal(&destinationNode)
+}
+
+func traverseAndCompare(sourceNode, destinationNode *yaml.Node, path string) error {
+	if sourceNode.Kind != destinationNode.Kind {
+		return fmt.Errorf("Type mismatch at %s: %s vs %s\n", path, nodeKindToString(sourceNode.Kind), nodeKindToString(destinationNode.Kind))
+	}
+
+	switch sourceNode.Kind {
+	case yaml.ScalarNode:
+		if sourceNode.Value != destinationNode.Value {
+			destinationNode.Value = sourceNode.Value
+		}
+
+	case yaml.MappingNode:
+		map1 := mapNodeToMap(sourceNode)
+		map2 := mapNodeToMap(destinationNode)
+
+		allKeys := getAllKeys(map1, map2)
+
+		for _, key := range allKeys {
+			var childPath string
+			if path == "" {
+				childPath = key
+			} else {
+				childPath = path + "." + key
+			}
+
+			sourceNodeChild, ok1 := map1[key]
+			destinationNodeChild, ok2 := map2[key]
+
+			if !ok1 || !ok2 {
+				destinationNode.Content = sourceNode.Content
+			} else {
+				err := traverseAndCompare(sourceNodeChild, destinationNodeChild, childPath)
+				if err != nil {
+					return err
+				}
+			}
+		}
+
+	case yaml.SequenceNode:
+		sourceLen := len(sourceNode.Content)
+		destinationLen := len(destinationNode.Content)
+
+		maxLen := sourceLen
+		if destinationLen > maxLen {
+			maxLen = destinationLen
+		}
+
+		for i := 0; i < maxLen; i++ {
+			childPath := fmt.Sprintf("%s[%d]", path, i)
+
+			if i >= destinationLen {
+				destinationNode.Content = append(destinationNode.Content, sourceNode.Content[i])
+			} else if i < sourceLen {
+				err := traverseAndCompare(sourceNode.Content[i], destinationNode.Content[i], childPath)
+				if err != nil {
+					return err
+				}
+			}
+		}
+	}
+	return nil
+}
+
+func mapNodeToMap(node *yaml.Node) map[string]*yaml.Node {
+	result := make(map[string]*yaml.Node)
+	for i := 0; i < len(node.Content); i += 2 {
+		keyNode := node.Content[i]
+		valueNode := node.Content[i+1]
+		result[keyNode.Value] = valueNode
+	}
+	return result
+}
+
+func getAllKeys(map1, map2 map[string]*yaml.Node) []string {
+	keys := make(map[string]struct{})
+	for key := range map1 {
+		keys[key] = struct{}{}
+	}
+	for key := range map2 {
+		keys[key] = struct{}{}
+	}
+
+	var keyList []string
+	for key := range keys {
+		keyList = append(keyList, key)
+	}
+	return keyList
+}
+
+func nodeKindToString(kind yaml.Kind) string {
+	switch kind {
+	case yaml.ScalarNode:
+		return "Scalar"
+	case yaml.MappingNode:
+		return "Mapping"
+	case yaml.SequenceNode:
+		return "Sequence"
+	default:
+		return "Unknown"
+	}
+}
diff --git a/pkg/migrate/overwrite_yaml_test.go b/pkg/migrate/overwrite_yaml_test.go
new file mode 100644
index 0000000000..280781c72b
--- /dev/null
+++ b/pkg/migrate/overwrite_yaml_test.go
@@ -0,0 +1,64 @@
+package migrate
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestOverwrightYAML(t *testing.T) {
+	var yamlData1 = `build:
+    command: "build.sh"
+image: "my-image"
+predict: "predict.py"
+train: "train.py"
+concurrency:
+    max: 5
+environment:
+    - "VAR1=value1"
+    - "VAR2=value2"
+`
+
+	var yamlData2 = `build:
+  command: "build_new.sh"
+image: "new-image"
+predict: "new_predict.py"
+concurrency:
+  max: 10
+environment:
+  - "VAR1=new_value1"
+  - "VAR3=value3"
+`
+	content, err := OverwrightYAML([]byte(yamlData1), []byte(yamlData2))
+	require.NoError(t, err)
+	require.Equal(t, yamlData1, string(content))
+}
+
+func TestOverwrightYAMLWithComments(t *testing.T) {
+	var yamlData1 = `# This here is a YAML Comment
+build:
+    command: "build.sh"
+image: "my-image"
+predict: "predict.py"
+train: "train.py"
+concurrency:
+    max: 5
+environment:
+    - "VAR1=value1"
+    - "VAR2=value2"
+`
+
+	var yamlData2 = `build:
+  command: "build_new.sh"
+image: "new-image"
+predict: "new_predict.py"
+concurrency:
+  max: 10
+environment:
+  - "VAR1=new_value1"
+  - "VAR3=value3"
+`
+	content, err := OverwrightYAML([]byte(yamlData1), []byte(yamlData2))
+	require.NoError(t, err)
+	require.Equal(t, yamlData1, string(content))
+}