diff --git a/CHANGELOG.md b/CHANGELOG.md
index 74cee70..8b0894e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,13 @@
 
 ##### Bug Fixes
 
-* None.  
+* When downloading git submodules, use an explicit command (`git submodules
+  --init --recursive`) instead of relying on the `--recursive` behavior for
+  `git checkout`. This fixes an issue where submodules were checked out using
+  `--depth=1` under git 2.9.  
+  [Gordon Fontenot](https://github.com/gfontenot)
+  [#58](https://github.com/CocoaPods/cocoapods-downloader/pull/58)
+  [CocoaPods#5555](https://github.com/CocoaPods/CocoaPods/issues/5555)
 
 
 ## 1.0.0 (2016-05-10)
diff --git a/lib/cocoapods-downloader/git.rb b/lib/cocoapods-downloader/git.rb
index be96a80..428b8ba 100644
--- a/lib/cocoapods-downloader/git.rb
+++ b/lib/cocoapods-downloader/git.rb
@@ -62,6 +62,12 @@ def clone(force_head = false, shallow_clone = true)
         ui_sub_action('Git download') do
           begin
             git! clone_arguments(force_head, shallow_clone)
+
+            if options[:submodules]
+              Dir.chdir(target_path) do
+                git! %w(submodule update --init --recursive)
+              end
+            end
           rescue DownloaderError => e
             if e.message =~ /^fatal:.*does not support --depth$/im
               clone(force_head, false)
@@ -97,8 +103,6 @@ def clone_arguments(force_head, shallow_clone)
           end
         end
 
-        command << '--recursive' if options[:submodules]
-
         command
       end