diff --git a/apps/files/admin.php b/apps/files/admin.php
index 70f537d0db..349c27ff74 100644
--- a/apps/files/admin.php
+++ b/apps/files/admin.php
@@ -42,9 +42,10 @@ if($_POST && OC_Util::isCallRegistered()) {
 }
 
 $htaccessWritable=is_writable(OC::$SERVERROOT.'/.htaccess');
+$userIniWritable=is_writable(OC::$SERVERROOT.'/.user.ini');
 
 $tmpl = new OCP\Template( 'files', 'admin' );
-$tmpl->assign( 'uploadChangable', $htaccessWorking and $htaccessWritable );
+$tmpl->assign( 'uploadChangable', ($htaccessWorking and $htaccessWritable) or $userIniWritable );
 $tmpl->assign( 'uploadMaxFilesize', $maxUploadFilesize);
 // max possible makes only sense on a 32 bit system
 $tmpl->assign( 'displayMaxPossibleUploadSize', PHP_INT_SIZE===4);
diff --git a/apps/files/templates/admin.php b/apps/files/templates/admin.php
index adf756a12b..822fc779bd 100644
--- a/apps/files/templates/admin.php
+++ b/apps/files/templates/admin.php
@@ -10,6 +10,8 @@
 		<br/>
 		<input type="hidden" value="<?php p($_['requesttoken']); ?>" name="requesttoken" />
 		<?php if($_['uploadChangable']): ?>
+			<?php p($l->t('With PHP-FPM this value may take up to 5 minutes to take effect after saving.')); ?>
+			<br/>
 			<input type="submit" name="submitFilesAdminSettings" id="submitFilesAdminSettings"
 				   value="<?php p($l->t( 'Save' )); ?>"/>
 		<?php else: ?>
diff --git a/lib/private/files.php b/lib/private/files.php
index b61d09d8a0..b9fd109331 100644
--- a/lib/private/files.php
+++ b/lib/private/files.php
@@ -21,6 +21,7 @@
  * @author Thomas Müller <thomas.mueller@tmit.eu>
  * @author Valerio Ponte <valerio.ponte@gmail.com>
  * @author Vincent Petry <pvince81@owncloud.com>
+ * @author Robin McCorkell <rmccorkell@karoshi.org.uk>
  *
  * @copyright Copyright (c) 2015, ownCloud, Inc.
  * @license AGPL-3.0
@@ -288,38 +289,63 @@ class OC_Files {
 			return false;
 		}
 
-		//suppress errors in case we don't have permissions for
-		$htaccess = @file_get_contents(OC::$SERVERROOT . '/.htaccess');
-		if (!$htaccess) {
-			return false;
-		}
-
 		$phpValueKeys = array(
 			'upload_max_filesize',
 			'post_max_size'
 		);
 
-		foreach ($phpValueKeys as $key) {
-			$pattern = '/php_value ' . $key . ' (\S)*/';
-			$setting = 'php_value ' . $key . ' ' . $size;
-			$hasReplaced = 0;
-			$content = preg_replace($pattern, $setting, $htaccess, 1, $hasReplaced);
-			if ($content !== null) {
-				$htaccess = $content;
+		$updateFiles = [
+			OC::$SERVERROOT . '/.htaccess' => [
+				'pattern' => '/php_value %1$s (\S)*/',
+				'setting' => 'php_value %1$s %2$s'
+			],
+			OC::$SERVERROOT . '/.user.ini' => [
+				'pattern' => '/%1$s=(\S)*/',
+				'setting' => '%1$s=%2$s'
+			]
+		];
+
+		$success = true;
+
+		foreach ($updateFiles as $filename => $patternMap) {
+			// suppress warnings from fopen()
+			$handle = @fopen($filename, 'r+');
+			if (!$handle) {
+				\OCP\Util::writeLog('files',
+					'Can\'t write upload limit to ' . $filename . '. Please check the file permissions',
+					\OCP\Util::WARN);
+				$success = false;
+				continue; // try to update as many files as possible
 			}
-			if ($hasReplaced === 0) {
-				$htaccess .= "\n" . $setting;
+
+			$content = '';
+			while (!feof($handle)) {
+				$content .= fread($handle, 1000);
 			}
+
+			foreach ($phpValueKeys as $key) {
+				$pattern = vsprintf($patternMap['pattern'], [$key]);
+				$setting = vsprintf($patternMap['setting'], [$key, $size]);
+				$hasReplaced = 0;
+				$newContent = preg_replace($pattern, $setting, $content, 1, $hasReplaced);
+				if ($newContent !== null) {
+					$content = $newContent;
+				}
+				if ($hasReplaced === 0) {
+					$content .= "\n" . $setting;
+				}
+			}
+
+			// write file back
+			ftruncate($handle, 0);
+			rewind($handle);
+			fwrite($handle, $content);
+
+			fclose($handle);
 		}
 
-		//check for write permissions
-		if (is_writable(OC::$SERVERROOT . '/.htaccess')) {
-			file_put_contents(OC::$SERVERROOT . '/.htaccess', $htaccess);
+		if ($success) {
 			return OC_Helper::computerFileSize($size);
-		} else {
-			\OCP\Util::writeLog('files',
-				'Can\'t write upload limit to ' . OC::$SERVERROOT . '/.htaccess. Please check the file permissions',
-				\OCP\Util::WARN);
 		}
 		return false;
 	}