diff --git a/src/PHPSemVerChecker/Console/Command/BaseCommand.php b/src/PHPSemVerChecker/Console/Command/BaseCommand.php
index f098e9a..84fede8 100644
--- a/src/PHPSemVerChecker/Console/Command/BaseCommand.php
+++ b/src/PHPSemVerChecker/Console/Command/BaseCommand.php
@@ -26,7 +26,7 @@ protected function initialize(InputInterface $input, OutputInterface $output)
 		$configPath = $input->getOption('config');
 		$this->config = $configPath ? Configuration::fromFile($configPath) : Configuration::defaults('php-semver-checker');
 		$inputMerger = new InputMerger();
-		$inputMerger->merge($input, $this->config);
+		$inputMerger->merge($input, $this->getDefinition(), $this->config);
 
 		// Set overrides
 		LevelMapping::setOverrides($this->config->getLevelMapping());
diff --git a/src/PHPSemVerChecker/Console/InputMerger.php b/src/PHPSemVerChecker/Console/InputMerger.php
index b7fb249..28d10e2 100644
--- a/src/PHPSemVerChecker/Console/InputMerger.php
+++ b/src/PHPSemVerChecker/Console/InputMerger.php
@@ -3,6 +3,7 @@
 namespace PHPSemVerChecker\Console;
 
 use PHPSemVerChecker\Configuration\Configuration;
+use Symfony\Component\Console\Input\InputDefinition;
 use Symfony\Component\Console\Input\InputInterface;
 
 /**
@@ -14,24 +15,34 @@
 class InputMerger
 {
 	/**
-	 * @param \Symfony\Component\Console\Input\InputInterface $input
-	 * @param \PHPSemVerChecker\Configuration\Configuration $config
+	 * @param \Symfony\Component\Console\Input\InputInterface  $input           Actual input
+	 * @param \Symfony\Component\Console\Input\InputDefinition $inputDefinition Definition of input arguments/options
+	 * @param \PHPSemVerChecker\Configuration\Configuration    $config
 	 */
-	public function merge(InputInterface $input, Configuration $config)
+	public function merge(InputInterface $input, InputDefinition $inputDefinition, Configuration $config)
 	{
 		foreach ($input->getArguments() as $argument => $value) {
-			if ($input->hasArgumentSet($argument)) {
+			if ($value !== null) {
 				$config->set($argument, $value);
 			} else {
-				$input->setArgument($argument, $config->get($argument));
+				$configValue = $config->get($argument);
+				// Only set an argument from config if actually known
+				if ($configValue !== null) {
+					$input->setArgument($argument, $configValue);
+				}
 			}
 		}
 
-		foreach ($input->getOptions() as $option => $value) {
-			if ($input->hasOptionSet($option)) {
-				$config->set($option, $value);
+		foreach ($input->getOptions() as $optionName => $value) {
+			$option = $inputDefinition->getOption($optionName);
+			// Make sure VALUE_NONE is only used when differing from default
+			if ((!$option->acceptValue() && $value !== $option->getDefault()) || ($option->acceptValue() && $value !== null)) {
+				$config->set($optionName, $value);
 			} else {
-				$input->setOption($option, $config->get($option));
+				$configValue = $config->get($optionName);
+				if ($configValue !== null) {
+					$input->setOption($optionName, $configValue);
+				}
 			}
 		}
 	}
diff --git a/tests/PHPSemVerChecker/Console/InputMergerTest.php b/tests/PHPSemVerChecker/Console/InputMergerTest.php
index c375d1a..7e0230b 100644
--- a/tests/PHPSemVerChecker/Console/InputMergerTest.php
+++ b/tests/PHPSemVerChecker/Console/InputMergerTest.php
@@ -25,7 +25,7 @@ public function testMerge()
 		$this->assertEquals('in-before cli', $input->getOption('include-before'), 'Test setup: Could not prepare input arguments');
 
 		$im = new InputMerger();
-		$im->merge($input, $config);
+		$im->merge($input, $command->getDefinition(), $config);
 		$this->assertEquals('in-before cli', $config->get('include-before'), 'Configuration must be overwritten by CLI option');
 		$this->assertEquals('src-before cli', $config->get('source-before'), 'Configuration must be overwritten by CLI argument');
 		$this->assertEquals('src-before cli', $input->getArgument('source-before'), 'Input arguments must not be overwritten by empty configuration');
@@ -33,4 +33,20 @@ public function testMerge()
 		$this->assertEquals('src-after config', $input->getArgument('source-after'), 'Missing input arguments must take on existing configuration');
 		$this->assertEquals(true, $config->get('full-path'), 'CLI option should use Configuration value and not CLI default');
 	}
+
+	/**
+	 * @expectedException \Symfony\Component\Console\Exception\RuntimeException
+	 */
+	public function testEmptyInputShouldThrowException()
+	{
+		// Default/empty configuration
+		$config = new Configuration([]);
+		// No input arguments
+		$input = new InspectableArgvInput([null]);
+		$command = new CompareCommand();
+		$input->bind($command->getDefinition());
+		$im = new InputMerger();
+		$im->merge($input, $command->getDefinition(), $config);
+		$input->validate();
+	}
 }