diff --git a/pkg/config/config.go b/pkg/config/config.go
index 9222dea..625cff3 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -47,7 +47,7 @@ func Init() {
 }
 
 func NewConfiguration() (*port.Config, error) {
-	overrides := &port.Config{
+	config := &port.Config{
 		StateKey:                        ApplicationConfig.StateKey,
 		EventListenerType:               ApplicationConfig.EventListenerType,
 		CreateDefaultResources:          ApplicationConfig.CreateDefaultResources,
@@ -61,15 +61,15 @@ func NewConfiguration() (*port.Config, error) {
 	if err != nil {
 		v = []byte("{}")
 		klog.Infof("Config file not found, using defaults")
-		return overrides, nil
+		return config, nil
 	}
 	klog.Infof("Config file found")
-	err = yaml.Unmarshal(v, &overrides)
+	err = yaml.Unmarshal(v, &config)
 	if err != nil {
 		return nil, fmt.Errorf("failed loading configuration: %w", err)
 	}
 
-	overrides.StateKey = strings.ToLower(overrides.StateKey)
+	config.StateKey = strings.ToLower(config.StateKey)
 
-	return overrides, nil
+	return config, nil
 }
diff --git a/pkg/config/models.go b/pkg/config/models.go
index 05d94d1..8020d39 100644
--- a/pkg/config/models.go
+++ b/pkg/config/models.go
@@ -22,10 +22,8 @@ type ApplicationConfiguration struct {
 	EventListenerType               string
 	CreateDefaultResources          bool
 	OverwriteConfigurationOnRestart bool
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
-	Resources []port.Resource
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
-	DeleteDependents bool `json:"deleteDependents,omitempty"`
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
+	// These Configurations are used only for setting up the Integration on installation or when using OverwriteConfigurationOnRestart flag.
+	Resources                    []port.Resource
+	DeleteDependents             bool `json:"deleteDependents,omitempty"`
 	CreateMissingRelatedEntities bool `json:"createMissingRelatedEntities,omitempty"`
 }
diff --git a/pkg/defaults/defaults_test.go b/pkg/defaults/defaults_test.go
index 7a7c07e..a0ff870 100644
--- a/pkg/defaults/defaults_test.go
+++ b/pkg/defaults/defaults_test.go
@@ -192,7 +192,7 @@ func Test_InitIntegration_ExistingIntegration(t *testing.T) {
 	checkResourcesDoesNotExist(f, []string{"workload", "namespace", "cluster"}, []string{"workload_overview_dashboard", "availability_scorecard_dashboard"})
 }
 
-func Test_InitIntegration_DeprecatedResourcesConfiguration(t *testing.T) {
+func Test_InitIntegration_LocalResourcesConfiguration(t *testing.T) {
 	f := NewFixture(t)
 	err := integration.CreateIntegration(f.portClient, f.stateKey, "", nil)
 	if err != nil {
@@ -233,7 +233,7 @@ func Test_InitIntegration_DeprecatedResourcesConfiguration(t *testing.T) {
 	checkResourcesDoesNotExist(f, []string{"workload", "namespace", "cluster"}, []string{"workload_overview_dashboard", "availability_scorecard_dashboard"})
 }
 
-func Test_InitIntegration_DeprecatedResourcesConfiguration_ExistingIntegration_EmptyConfiguration(t *testing.T) {
+func Test_InitIntegration_LocalResourcesConfiguration_ExistingIntegration_EmptyConfiguration(t *testing.T) {
 	f := NewFixture(t)
 	err := integration.CreateIntegration(f.portClient, f.stateKey, "POLLING", nil)
 	if err != nil {
@@ -253,3 +253,49 @@ func Test_InitIntegration_DeprecatedResourcesConfiguration_ExistingIntegration_E
 
 	checkResourcesDoesNotExist(f, []string{"workload", "namespace", "cluster"}, []string{"workload_overview_dashboard", "availability_scorecard_dashboard"})
 }
+
+func Test_InitIntegration_LocalResourcesConfiguration_ExistingIntegration_WithConfiguration_WithOverwriteConfigurationOnRestartFlag(t *testing.T) {
+	f := NewFixture(t)
+	expectedResources := &port.IntegrationAppConfig{
+		Resources: []port.Resource{
+			{
+				Kind: "workload",
+				Port: port.Port{
+					Entity: port.EntityMappings{
+						Mappings: []port.EntityMapping{
+							{
+								Identifier: "\"workload\"",
+								Title:      "\"Workload\"",
+								Blueprint:  "\"workload\"",
+								Icon:       "\"Microservice\"",
+								Properties: map[string]string{
+									"namespace": "\"default\"",
+								},
+							},
+						},
+					},
+				},
+			},
+		},
+	}
+	err := integration.CreateIntegration(f.portClient, f.stateKey, "POLLING", expectedResources)
+	if err != nil {
+		t.Errorf("Error creating Port integration: %s", err.Error())
+	}
+
+	expectedResources.Resources[0].Kind = "namespace"
+	e := InitIntegration(f.portClient, &port.Config{
+		StateKey:                        f.stateKey,
+		EventListenerType:               "KAFKA",
+		Resources:                       expectedResources.Resources,
+		CreateDefaultResources:          true,
+		OverwriteConfigurationOnRestart: true,
+	})
+	assert.Nil(t, e)
+
+	i, err := integration.GetIntegration(f.portClient, f.stateKey)
+	assert.Nil(t, err)
+	assert.Equal(t, expectedResources, i.Config.Resources)
+
+	checkResourcesDoesNotExist(f, []string{"workload", "namespace", "cluster"}, []string{"workload_overview_dashboard", "availability_scorecard_dashboard"})
+}
diff --git a/pkg/port/models.go b/pkg/port/models.go
index 28a838a..57d1966 100644
--- a/pkg/port/models.go
+++ b/pkg/port/models.go
@@ -227,15 +227,13 @@ type IntegrationAppConfig struct {
 }
 
 type Config struct {
-	ResyncInterval                  uint   `yaml:"resyncInterval,omitempty" json:"resyncInterval,omitempty"`
-	StateKey                        string `yaml:"stateKey,omitempty" json:"stateKey,omitempty"`
-	EventListenerType               string `yaml:"eventListenerType,omitempty" json:"eventListenerType,omitempty"`
-	CreateDefaultResources          bool   `yaml:"createDefaultResources,omitempty" json:"createDefaultResources,omitempty"`
-	OverwriteConfigurationOnRestart bool   `yaml:"overwriteConfigurationOnRestart,omitempty" json:"overwriteConfigurationOnRestart,omitempty"`
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
-	Resources []Resource `yaml:"resources,omitempty" json:"resources,omitempty"`
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
-	DeleteDependents bool `yaml:"deleteDependents,omitempty" json:"deleteDependents,omitempty"`
-	// Deprecated: use IntegrationAppConfig instead. Used for updating the Port integration config on startup.
-	CreateMissingRelatedEntities bool `yaml:"createMissingRelatedEntities,omitempty" json:"createMissingRelatedEntities,omitempty"`
+	ResyncInterval                  uint   `yaml:"resyncInterval,omitempty"`
+	StateKey                        string `yaml:"stateKey,omitempty"`
+	EventListenerType               string `yaml:"eventListenerType,omitempty"`
+	CreateDefaultResources          bool   `yaml:"createDefaultResources,omitempty"`
+	OverwriteConfigurationOnRestart bool   `yaml:"overwriteConfigurationOnRestart,omitempty"`
+	// These Configurations are used only for setting up the Integration on installation or when using OverwriteConfigurationOnRestart flag.
+	Resources                    []Resource `yaml:"resources,omitempty"`
+	DeleteDependents             bool       `yaml:"deleteDependents,omitempty"`
+	CreateMissingRelatedEntities bool       `yaml:"createMissingRelatedEntities,omitempty"`
 }