diff --git a/lib/private/Config.php b/lib/private/Config.php
index ecfb9fc3160..ddcc6e1179b 100644
--- a/lib/private/Config.php
+++ b/lib/private/Config.php
@@ -35,7 +35,8 @@ class Config {
  */
 ";
 
-	protected array $cache = [];
+	protected array $mergedCache = [];
+	protected array $cacheByPath = [];
 	protected array $envCache = [];
 	protected string $configFilePath;
 	protected bool $isReadOnly;
@@ -61,7 +62,7 @@ class Config {
 	 * @return array an array of key names
 	 */
 	public function getKeys(): array {
-		return array_merge(array_keys($this->cache), array_keys($this->envCache));
+		return array_merge(array_keys($this->mergedCache), array_keys($this->envCache));
 	}
 
 	/**
@@ -80,8 +81,8 @@ class Config {
 			return self::trustSystemConfig($this->envCache[$key]);
 		}
 
-		if (isset($this->cache[$key])) {
-			return self::trustSystemConfig($this->cache[$key]);
+		if (isset($this->mergedCache[$key])) {
+			return self::trustSystemConfig($this->mergedCache[$key]);
 		}
 
 		return $default;
@@ -153,9 +154,10 @@ class Config {
 	 * @throws HintException
 	 */
 	protected function set($key, $value) {
-		if (!isset($this->cache[$key]) || $this->cache[$key] !== $value) {
+		if (!isset($this->mergedCache[$key]) || $this->mergedCache[$key] !== $value) {
 			// Add change
-			$this->cache[$key] = $value;
+			$this->mergedCache[$key] = $value;
+			$this->cacheByPath[$this->configFilePath][$key] = $value;
 			return true;
 		}
 
@@ -183,9 +185,9 @@ class Config {
 	 * @throws HintException
 	 */
 	protected function delete($key) {
-		if (isset($this->cache[$key])) {
+		if (isset($this->mergedCache[$key])) {
 			// Delete key from cache
-			unset($this->cache[$key]);
+			unset($this->mergedCache[$key], $this->cacheByPath[$this->configFilePath][$key]);
 			return true;
 		}
 		return false;
@@ -254,7 +256,8 @@ class Config {
 				throw new \Exception($errorMessage);
 			}
 			if (isset($CONFIG) && is_array($CONFIG)) {
-				$this->cache = array_replace_recursive($this->cache, $CONFIG);
+				$this->mergedCache = array_replace_recursive($this->mergedCache, $CONFIG);
+				$this->cacheByPath[$file] = $CONFIG;
 			}
 		}
 
@@ -281,22 +284,25 @@ class Config {
 	private function writeData(): void {
 		$this->checkReadOnly();
 
-		if (!is_file(\OC::$configDir . '/CAN_INSTALL') && !isset($this->cache['version'])) {
+		if (!is_file(\OC::$configDir . '/CAN_INSTALL') && !isset($this->mergedCache['version'])) {
 			throw new HintException(sprintf('Configuration was not read or initialized correctly, not overwriting %s', $this->configFilePath));
 		}
 
+		// Only save the values to config.php that originally came from it or were added in the current process.
+		$values = $this->cacheByPath[$this->configFilePath];
+
 		// Create a php file ...
 		$content = "<?php\n";
 		$content .= self::CONF_WARNING;
 		$content .= '$CONFIG = ';
-		$content .= var_export(self::trustSystemConfig($this->cache), true);
+		$content .= var_export(self::trustSystemConfig($values), true);
 		$content .= ";\n";
 
 		touch($this->configFilePath);
 		$filePointer = fopen($this->configFilePath, 'r+');
 
 		// Apply permissions for config.php, defaulting to user read-write and group read
-		$permissions = $this->cache['configfilemode'] ?? 0640;
+		$permissions = $this->mergedCache['configfilemode'] ?? 0640;
 		chmod($this->configFilePath, $permissions);
 
 		// File does not exist, this can happen when doing a fresh install
diff --git a/tests/lib/ConfigTest.php b/tests/lib/ConfigTest.php
index c0a6e4bb53b..8c76ee41802 100644
--- a/tests/lib/ConfigTest.php
+++ b/tests/lib/ConfigTest.php
@@ -13,7 +13,7 @@ use OCP\ITempManager;
 use OCP\Server;
 
 class ConfigTest extends TestCase {
-	public const TESTCONTENT = '<?php $CONFIG=array("foo"=>"bar", "beers" => array("Appenzeller", "Guinness", "Kölsch"), "alcohol_free" => false);';
+	public const TESTCONTENT = '<?php $CONFIG=array("foo"=>"bar", "beers" => array("Appenzeller", "Guinness", "Kölsch"), "alcohol_free" => false, "top" => ["bottom1" => "value1"]);';
 
 	/** @var array */
 	private $initialConfig = ['foo' => 'bar', 'beers' => ['Appenzeller', 'Guinness', 'Kölsch'], 'alcohol_free' => false];
@@ -42,12 +42,12 @@ class ConfigTest extends TestCase {
 	}
 
 	public function testGetKeys(): void {
-		$expectedConfig = ['foo', 'beers', 'alcohol_free'];
+		$expectedConfig = ['foo', 'beers', 'alcohol_free', 'top'];
 		$this->assertSame($expectedConfig, $this->getConfig()->getKeys());
 	}
 
 	public function testGetKeysReturnsEnvironmentKeysIfSet() {
-		$expectedConfig = ['foo', 'beers', 'alcohol_free', 'taste'];
+		$expectedConfig = ['foo', 'beers', 'alcohol_free', 'top', 'taste'];
 		putenv('NC_taste=great');
 		$this->assertSame($expectedConfig, $this->getConfig()->getKeys());
 		putenv('NC_taste');
@@ -102,7 +102,7 @@ class ConfigTest extends TestCase {
 		$expected = "<?php\n";
 		$expected .= Config::CONF_WARNING;
 		$expected .= "\$CONFIG = array (\n  'foo' => 'moo',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
-			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n);\n";
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n);\n";
 		$this->assertEquals($expected, $content);
 
 		$config->setValue('bar', 'red');
@@ -115,7 +115,7 @@ class ConfigTest extends TestCase {
 		$expected = "<?php\n";
 		$expected .= Config::CONF_WARNING;
 		$expected .= "\$CONFIG = array (\n  'foo' => 'moo',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
-			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'bar' => 'red',\n  'apps' => \n "
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n  'bar' => 'red',\n  'apps' => \n "
 			. " array (\n    0 => 'files',\n    1 => 'gallery',\n  ),\n);\n";
 		$this->assertEquals($expected, $content);
 	}
@@ -148,7 +148,7 @@ class ConfigTest extends TestCase {
 		$expected = "<?php\n";
 		$expected .= Config::CONF_WARNING;
 		$expected .= "\$CONFIG = array (\n  'foo' => 'moo',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
-			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n);\n";
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n);\n";
 		$this->assertEquals($expected, $content);
 	}
 
@@ -161,13 +161,13 @@ class ConfigTest extends TestCase {
 		$expected = "<?php\n";
 		$expected .= Config::CONF_WARNING;
 		$expected .= "\$CONFIG = array (\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
-			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n);\n";
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n);\n";
 		$this->assertEquals($expected, $content);
 	}
 
 	public function testConfigMerge(): void {
 		// Create additional config
-		$additionalConfig = '<?php $CONFIG=array("php53"=>"totallyOutdated");';
+		$additionalConfig = '<?php $CONFIG=array("php53"=>"totallyOutdated","alcohol_free"=>true);';
 		$additionalConfigPath = $this->randomTmpDir . 'additionalConfig.testconfig.php';
 		file_put_contents($additionalConfigPath, $additionalConfig);
 
@@ -178,16 +178,75 @@ class ConfigTest extends TestCase {
 		$this->assertSame('totallyOutdated', $config->getValue('php53', 'bogusValue'));
 		$this->assertEquals(self::TESTCONTENT, file_get_contents($this->configFile));
 
+		// Value is overwritten by additional config file, but not saved to the main config file.
+		$this->assertTrue($config->getValue('alcohol_free'));
+
+		// Set a new key that's saved to the main config file
+		$config->setValue('new_key', 'new_value');
+
 		// Write a new value to the config
 		$config->setValue('CoolWebsites', ['demo.owncloud.org', 'owncloud.org', 'owncloud.com']);
 		$expected = "<?php\n";
 		$expected .= Config::CONF_WARNING;
 		$expected .= "\$CONFIG = array (\n  'foo' => 'bar',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
-			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'php53' => 'totallyOutdated',\n  'CoolWebsites' => \n  array (\n  "
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n  'new_key' => 'new_value',\n  'CoolWebsites' => \n  array (\n  "
 			. "  0 => 'demo.owncloud.org',\n    1 => 'owncloud.org',\n    2 => 'owncloud.com',\n  ),\n);\n";
 		$this->assertEquals($expected, file_get_contents($this->configFile));
 
 		// Cleanup
 		unlink($additionalConfigPath);
 	}
+
+	public function testConfigMergeRecursive(): void {
+		$additionalConfig = '<?php $CONFIG=["top" => ["bottom2" => "value2"]];';
+		$additionalConfigPath = $this->randomTmpDir . 'additionalConfig.testconfig.php';
+		file_put_contents($additionalConfigPath, $additionalConfig);
+
+		$config = new Config($this->randomTmpDir, 'testconfig.php');
+
+		// Values are merged correctly from the additional config file
+		$this->assertEquals(['bottom1' => 'value1', 'bottom2' => 'value2'], $config->getValue('top'));
+
+		self::invokePrivate($config, 'writeData');
+
+		// Values from the additional config file are not saved to the main config file
+		$expected = "<?php\n";
+		$expected .= Config::CONF_WARNING;
+		$expected .= "\$CONFIG = array (\n  'foo' => 'bar',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n);\n";
+		$this->assertEquals($expected, file_get_contents($this->configFile));
+
+		unlink($additionalConfigPath);
+	}
+
+	/**
+	 * The current behavior of additional config files is broken.
+	 * Setting or deleting a key in the current process will remove it from the main config file,
+	 * but if the key is specified in an additional config file it will just be overwritten again.
+	 */
+	public function testConfigAdditionalSetDelete(): void {
+		$additionalConfig = '<?php $CONFIG=["key1" => "value1", "key2" => "value2"];';
+		$additionalConfigPath = $this->randomTmpDir . 'additionalConfig.testconfig.php';
+		file_put_contents($additionalConfigPath, $additionalConfig);
+
+		$config = new Config($this->randomTmpDir, 'testconfig.php');
+
+		$config->setValue('key1', 'value3');
+		$config->deleteKey('key2');
+
+		// The updated config is written to the main config file
+		$expected = "<?php\n";
+		$expected .= Config::CONF_WARNING;
+		$expected .= "\$CONFIG = array (\n  'foo' => 'bar',\n  'beers' => \n  array (\n    0 => 'Appenzeller',\n  "
+			. "  1 => 'Guinness',\n    2 => 'Kölsch',\n  ),\n  'alcohol_free' => false,\n  'top' => \n  array (\n    'bottom1' => 'value1',\n  ),\n  'key1' => 'value3',\n);\n";
+		$this->assertEquals($expected, file_get_contents($this->configFile));
+
+		$config = new Config($this->randomTmpDir, 'testconfig.php');
+
+		// The additional config file overwrites the values again
+		$this->assertEquals('value1', $config->getValue('key1'));
+		$this->assertEquals('value2', $config->getValue('key2'));
+
+		unlink($additionalConfigPath);
+	}
 }