diff --git a/cmd/polaris/root.go b/cmd/polaris/root.go
index e1ee10da2..946e8d413 100644
--- a/cmd/polaris/root.go
+++ b/cmd/polaris/root.go
@@ -24,6 +24,7 @@ import (
 )
 
 var (
+	mergeConfig                  bool
 	configPath                   string
 	disallowExemptions           bool
 	disallowConfigExemptions     bool
@@ -42,6 +43,7 @@ var (
 
 func init() {
 	// Flags
+	rootCmd.PersistentFlags().BoolVarP(&mergeConfig, "merge-config", "m", false, "If true, custom configuration will be merged with default configuration instead of replacing it.")
 	rootCmd.PersistentFlags().StringVarP(&configPath, "config", "c", "", "Location of Polaris configuration file.")
 	rootCmd.PersistentFlags().StringVarP(&kubeContext, "context", "x", "", "Set the kube context.")
 	rootCmd.PersistentFlags().BoolVarP(&disallowExemptions, "disallow-exemptions", "", false, "Disallow any configured exemption.")
@@ -65,7 +67,7 @@ var rootCmd = &cobra.Command{
 			logrus.SetLevel(parsedLevel)
 		}
 
-		config, err = conf.ParseFile(configPath)
+		config, err = conf.MergeConfigAndParseFile(configPath, mergeConfig)
 		if err != nil {
 			logrus.Errorf("Error parsing config at %s: %v", configPath, err)
 			os.Exit(1)
diff --git a/pkg/config/config.go b/pkg/config/config.go
index 051473d5b..168872262 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -52,27 +52,50 @@ type Exemption struct {
 //go:embed default.yaml
 var defaultConfig []byte
 
-// ParseFile parses config from a file.
-func ParseFile(path string) (Configuration, error) {
-	var rawBytes []byte
+// MergeConfigAndParseFile parses config from a file.
+func MergeConfigAndParseFile(customConfigPath string, mergeConfig bool) (Configuration, error) {
+	rawBytes, err := mergeConfigFile(customConfigPath, mergeConfig)
+	if err != nil {
+		return Configuration{}, err
+	}
+
+	return Parse(rawBytes)
+}
+
+func mergeConfigFile(customConfigPath string, mergeConfig bool) ([]byte, error) {
+	if customConfigPath == "" {
+		return defaultConfig, nil
+	}
+
+	var customConfigContent []byte
 	var err error
-	if path == "" {
-		rawBytes = defaultConfig
-	} else if strings.HasPrefix(path, "https://") || strings.HasPrefix(path, "http://") {
+	if strings.HasPrefix(customConfigPath, "https://") || strings.HasPrefix(customConfigPath, "http://") {
 		// path is a url
-		response, err2 := http.Get(path)
-		if err2 != nil {
-			return Configuration{}, err2
+		response, err := http.Get(customConfigPath)
+		if err != nil {
+			return nil, err
+		}
+		customConfigContent, err = io.ReadAll(response.Body)
+		if err != nil {
+			return nil, err
 		}
-		rawBytes, err = io.ReadAll(response.Body)
 	} else {
 		// path is local
-		rawBytes, err = os.ReadFile(path)
+		customConfigContent, err = os.ReadFile(customConfigPath)
+		if err != nil {
+			return nil, err
+		}
 	}
-	if err != nil {
-		return Configuration{}, err
+
+	if mergeConfig {
+		mergedConfig, err := mergeYaml(defaultConfig, customConfigContent)
+		if err != nil {
+			return nil, err
+		}
+		return mergedConfig, nil
 	}
-	return Parse(rawBytes)
+
+	return customConfigContent, nil
 }
 
 // Parse parses config from a byte array.
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index cd7417492..5ad91f32a 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -125,7 +125,7 @@ func TestConfigFromURL(t *testing.T) {
 	}()
 	time.Sleep(time.Second)
 
-	parsedConf, err = ParseFile("http://localhost:8081/exampleURL")
+	parsedConf, err = MergeConfigAndParseFile("http://localhost:8081/exampleURL", false)
 	assert.NoError(t, err, "Expected no error when parsing YAML from URL")
 	if err := srv.Shutdown(context.TODO()); err != nil {
 		panic(err)
@@ -136,7 +136,7 @@ func TestConfigFromURL(t *testing.T) {
 
 func TestConfigNoServerError(t *testing.T) {
 	var err error
-	_, err = ParseFile("http://localhost:8081/exampleURL")
+	_, err = MergeConfigAndParseFile("http://localhost:8081/exampleURL", false)
 	assert.Error(t, err)
 	assert.Regexp(t, regexp.MustCompile("connection refused"), err.Error())
 }
diff --git a/pkg/config/merger.go b/pkg/config/merger.go
new file mode 100644
index 000000000..36003e255
--- /dev/null
+++ b/pkg/config/merger.go
@@ -0,0 +1,45 @@
+package config
+
+import (
+	"gopkg.in/yaml.v3" // do not change the yaml import
+)
+
+func mergeYaml(defaultConfig, overridesConfig []byte) ([]byte, error) {
+	var defaultData, overrideConfig map[string]any
+
+	err := yaml.Unmarshal([]byte(defaultConfig), &defaultData)
+	if err != nil {
+		return nil, err
+	}
+
+	err = yaml.Unmarshal([]byte(overridesConfig), &overrideConfig)
+	if err != nil {
+		return nil, err
+	}
+
+	mergedData := mergeYAMLMaps(defaultData, overrideConfig)
+
+	mergedConfig, err := yaml.Marshal(mergedData)
+	if err != nil {
+		return nil, err
+	}
+
+	return mergedConfig, nil
+}
+
+func mergeYAMLMaps(defaults, overrides map[string]any) map[string]any {
+	for k, v := range overrides {
+		if vMap, ok := v.(map[string]any); ok {
+			// if the key exists in defaults and is a map, recursively merge
+			if mv1, ok := defaults[k].(map[string]any); ok {
+				defaults[k] = mergeYAMLMaps(mv1, vMap)
+			} else {
+				defaults[k] = vMap
+			}
+		} else {
+			// add or overwrite the value in defaults
+			defaults[k] = v
+		}
+	}
+	return defaults
+}
diff --git a/pkg/config/merger_test.go b/pkg/config/merger_test.go
new file mode 100644
index 000000000..4f1df6711
--- /dev/null
+++ b/pkg/config/merger_test.go
@@ -0,0 +1,50 @@
+package config
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+var defaults = `
+checks:
+  deploymentMissingReplicas: warning
+  priorityClassNotSet: warning
+  tagNotSpecified: danger
+existing:
+  sub:
+    key: value
+`
+
+var overrides = `
+checks:
+  pullPolicyNotAlways: ignore
+  tagNotSpecified: overrides
+existing:
+  sub:
+    key1: value1
+  new: value
+new:
+  key: value
+`
+
+func TestMergeYaml(t *testing.T) {
+	mergedContent, err := mergeYaml([]byte(defaults), []byte(overrides))
+	assert.NoError(t, err)
+
+	expectedYAML := `checks:
+    deploymentMissingReplicas: warning
+    priorityClassNotSet: warning
+    pullPolicyNotAlways: ignore
+    tagNotSpecified: overrides
+existing:
+    new: value
+    sub:
+        key: value
+        key1: value1
+new:
+    key: value
+`
+
+	assert.Equal(t, expectedYAML, string(mergedContent))
+}