diff --git a/app/code/Magento/Payment/Plugin/PaymentConfigurationProcess.php b/app/code/Magento/Payment/Plugin/PaymentConfigurationProcess.php
index b1e36b7ae39f3..5b107b74295b3 100644
--- a/app/code/Magento/Payment/Plugin/PaymentConfigurationProcess.php
+++ b/app/code/Magento/Payment/Plugin/PaymentConfigurationProcess.php
@@ -59,10 +59,9 @@ public function beforeProcess(\Magento\Checkout\Block\Checkout\LayoutProcessor $
         $activePaymentMethodCodes = array_map($getCodeFunc, $activePaymentMethodList);
 
         foreach ($configuration as $paymentGroup => $groupConfig) {
-            foreach (array_keys($groupConfig['methods']) as $paymentCode) {
-                if (!in_array($paymentCode, $activePaymentMethodCodes)) {
-                    unset($configuration[$paymentGroup]['methods'][$paymentCode]);
-                }
+            $notActivePaymentMethodCodes = array_diff(array_keys($groupConfig['methods']), $activePaymentMethodCodes);
+            foreach ($notActivePaymentMethodCodes as $notActivePaymentMethodCode) {
+                unset($configuration[$paymentGroup]['methods'][$notActivePaymentMethodCode]);
             }
             if (empty($configuration[$paymentGroup]['methods'])) {
                 unset($configuration[$paymentGroup]);
diff --git a/app/code/Magento/Payment/Test/Unit/Plugin/PaymentConfigurationProcessTest.php b/app/code/Magento/Payment/Test/Unit/Plugin/PaymentConfigurationProcessTest.php
index be5755440066e..3e49c8718e604 100644
--- a/app/code/Magento/Payment/Test/Unit/Plugin/PaymentConfigurationProcessTest.php
+++ b/app/code/Magento/Payment/Test/Unit/Plugin/PaymentConfigurationProcessTest.php
@@ -98,6 +98,23 @@ public function testBeforeProcess($jsLayout, $activePaymentList, $expectedResult
     public function beforeProcessDataProvider()
     {
         $jsLayout['components']['checkout']['children']['steps']['children']['billing-step']
+        ['children']['payment']['children']['renders']['children'] = [
+            'braintree' => [
+                'methods' => [
+                    'braintree_paypal' => [],
+                    'braintree' => []
+                ]
+            ],
+            'paypal-payments' => [
+                'methods' => [
+                    'payflowpro' => [],
+                    'payflow_link' => []
+                ]
+            ]
+        ];
+        $result1['components']['checkout']['children']['steps']['children']['billing-step']
+        ['children']['payment']['children']['renders']['children'] = [];
+        $result2['components']['checkout']['children']['steps']['children']['billing-step']
         ['children']['payment']['children']['renders']['children'] = [
             'braintree' => [
                 'methods' => [
@@ -106,8 +123,6 @@ public function beforeProcessDataProvider()
                 ]
             ]
         ];
-        $result['components']['checkout']['children']['steps']['children']['billing-step']
-        ['children']['payment']['children']['renders']['children'] = [];
 
         $braintreePaymentMethod = $this
             ->getMockBuilder(\Magento\Payment\Api\Data\PaymentMethodInterface::class)
@@ -124,8 +139,8 @@ public function beforeProcessDataProvider()
         $braintreePaypalPaymentMethod->expects($this->any())->method('getCode')->willReturn('braintree_paypal');
 
         return [
-            [$jsLayout, [], $result],
-            [$jsLayout, [$braintreePaymentMethod, $braintreePaypalPaymentMethod], $jsLayout]
+            [$jsLayout, [], $result1],
+            [$jsLayout, [$braintreePaymentMethod, $braintreePaypalPaymentMethod], $result2]
         ];
     }
 }
diff --git a/app/code/Magento/Vault/Plugin/PaymentVaultConfigurationProcess.php b/app/code/Magento/Vault/Plugin/PaymentVaultConfigurationProcess.php
index 666e0b186309e..db38ccbed417a 100644
--- a/app/code/Magento/Vault/Plugin/PaymentVaultConfigurationProcess.php
+++ b/app/code/Magento/Vault/Plugin/PaymentVaultConfigurationProcess.php
@@ -69,21 +69,18 @@ public function beforeProcess(\Magento\Checkout\Block\Checkout\LayoutProcessor $
             return $method->getProviderCode();
         };
         $activePaymentMethodCodes = array_map($getCodeFunc, $activePaymentMethodList);
-        $activeVaultCodes = array_map($getCodeFunc, $activeVaultList);
         $activeVaultProviderCodes = array_map($getProviderCodeFunc, $activeVaultList);
         $activePaymentMethodCodes = array_merge(
             $activePaymentMethodCodes,
-            $activeVaultCodes,
             $activeVaultProviderCodes
         );
 
         foreach ($configuration as $paymentGroup => $groupConfig) {
-            foreach (array_keys($groupConfig['methods']) as $paymentCode) {
-                if (!in_array($paymentCode, $activePaymentMethodCodes)) {
-                    unset($configuration[$paymentGroup]['methods'][$paymentCode]);
-                }
+            $notActivePaymentMethodCodes = array_diff(array_keys($groupConfig['methods']), $activePaymentMethodCodes);
+            foreach ($notActivePaymentMethodCodes as $notActivePaymentMethodCode) {
+                unset($configuration[$paymentGroup]['methods'][$notActivePaymentMethodCode]);
             }
-            if ($paymentGroup === 'vault' && !empty($activeVaultCodes)) {
+            if ($paymentGroup === 'vault' && !empty($activeVaultProviderCodes)) {
                 continue;
             }
             if (empty($configuration[$paymentGroup]['methods'])) {
diff --git a/app/code/Magento/Vault/Test/Unit/Plugin/PaymentVaultConfigurationProcessTest.php b/app/code/Magento/Vault/Test/Unit/Plugin/PaymentVaultConfigurationProcessTest.php
index 0cf64c5424740..7e7a3fd0aebdf 100644
--- a/app/code/Magento/Vault/Test/Unit/Plugin/PaymentVaultConfigurationProcessTest.php
+++ b/app/code/Magento/Vault/Test/Unit/Plugin/PaymentVaultConfigurationProcessTest.php
@@ -112,9 +112,7 @@ public function beforeProcessDataProvider()
         $jsLayout['components']['checkout']['children']['steps']['children']['billing-step']
         ['children']['payment']['children']['renders']['children'] = [
             'vault' => [
-                'methods' => [
-                    'braintree_paypal_vault' => []
-                ]
+                'methods' => []
             ],
             'braintree' => [
                 'methods' => [
@@ -134,9 +132,7 @@ public function beforeProcessDataProvider()
         $result2['components']['checkout']['children']['steps']['children']['billing-step']
         ['children']['payment']['children']['renders']['children'] = [
             'vault' => [
-                'methods' => [
-                    'braintree_paypal_vault' => []
-                ]
+                'methods' => []
             ],
             'braintree' => [
                 'methods' => [
@@ -156,7 +152,7 @@ public function beforeProcessDataProvider()
 
         return [
             [$jsLayout, [], [], $result1],
-            [$jsLayout, [$vaultPaymentMethod], [], $result2]
+            [$jsLayout, [$vaultPaymentMethod], [$vaultPaymentMethod], $result2]
         ];
     }
 }