diff --git a/wp-admin/options-permalink.php b/wp-admin/options-permalink.php
index f77684129a..98a871d241 100644
--- a/wp-admin/options-permalink.php
+++ b/wp-admin/options-permalink.php
@@ -50,12 +50,21 @@ add_filter('admin_head', 'options_permalink_add_js');
 
 $home_path = get_home_path();
 $iis7_permalinks = iis7_supports_permalinks();
+$permalink_structure = get_option( 'permalink_structure' );
 
 $prefix = $blog_prefix = '';
 if ( ! got_url_rewrite() )
 	$prefix = '/index.php';
-if ( is_multisite() && !is_subdomain_install() && is_main_site() )
+
+/**
+ * In a subdirectory configuration of multisite, the `/blog` prefix is used by
+ * default on the main site to avoid collisions with other sites created on that
+ * network. If the `permalink_structure` option has been changed to remove this
+ * base prefix, WordPress core can no longer account for the possible collision.
+ */
+if ( is_multisite() && ! is_subdomain_install() && is_main_site() && 0 === strpos( $permalink_structure, '/blog/' ) ) {
 	$blog_prefix = '/blog';
+}
 
 if ( isset($_POST['permalink_structure']) || isset($_POST['category_base']) ) {
 	check_admin_referer('update-permalink');
@@ -94,7 +103,6 @@ if ( isset($_POST['permalink_structure']) || isset($_POST['category_base']) ) {
 	exit;
 }
 
-$permalink_structure = get_option( 'permalink_structure' );
 $category_base       = get_option( 'category_base' );
 $tag_base            = get_option( 'tag_base' );
 $update_required     = false;
@@ -162,7 +170,7 @@ if ( ! is_multisite() ) {
   <p><?php _e('By default WordPress uses web <abbr title="Universal Resource Locator">URL</abbr>s which have question marks and lots of numbers in them; however, WordPress offers you the ability to create a custom URL structure for your permalinks and archives. This can improve the aesthetics, usability, and forward-compatibility of your links. A <a href="https://codex.wordpress.org/Using_Permalinks">number of tags are available</a>, and here are some examples to get you started.'); ?></p>
 
 <?php
-if ( is_multisite() && !is_subdomain_install() && is_main_site() ) {
+if ( is_multisite() && ! is_subdomain_install() && is_main_site() && 0 === strpos( $permalink_structure, '/blog/' ) ) {
 	$permalink_structure = preg_replace( '|^/?blog|', '', $permalink_structure );
 	$category_base = preg_replace( '|^/?blog|', '', $category_base );
 	$tag_base = preg_replace( '|^/?blog|', '', $tag_base );
diff --git a/wp-includes/version.php b/wp-includes/version.php
index 6910bd9b7b..80bf66d9b4 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -4,7 +4,7 @@
  *
  * @global string $wp_version
  */
-$wp_version = '4.4-alpha-34748';
+$wp_version = '4.4-alpha-34749';
 
 /**
  * Holds the WordPress DB revision, increments when changes are made to the WordPress DB schema.