diff --git a/setup/src/Magento/Setup/Console/Command/ConfigSetCommand.php b/setup/src/Magento/Setup/Console/Command/ConfigSetCommand.php
index e8ff8f09c345e..9380a7b72d6b2 100644
--- a/setup/src/Magento/Setup/Console/Command/ConfigSetCommand.php
+++ b/setup/src/Magento/Setup/Console/Command/ConfigSetCommand.php
@@ -14,9 +14,6 @@
 use Symfony\Component\Console\Output\OutputInterface;
 use Symfony\Component\Console\Question\Question;
 
-/**
- * Config Set Command
- */
 class ConfigSetCommand extends AbstractSetupCommand
 {
     /**
@@ -72,6 +69,7 @@ protected function configure()
 
     /**
      * @inheritdoc
+     * @SuppressWarnings(PHPMD.CyclomaticComplexity)
      */
     protected function execute(InputInterface $input, OutputInterface $output)
     {
@@ -84,7 +82,10 @@ protected function execute(InputInterface $input, OutputInterface $output)
             $commandOptions[$option->getName()] = false;
 
             $currentValue = $this->deploymentConfig->get($option->getConfigPath());
-            if (($currentValue !== null) && ($inputOptions[$option->getName()] !== null)) {
+            $needOverwrite = ($currentValue !== null) &&
+                ($inputOptions[$option->getName()] !== null) &&
+                ($inputOptions[$option->getName()] !== $currentValue);
+            if ($needOverwrite) {
                 $dialog = $this->getHelperSet()->get('question');
                 $question = new Question(
                     '<question>Overwrite the existing configuration for ' . $option->getName() . '?[Y/n]</question>',