diff --git a/features/create_sites.feature b/features/create_sites.feature
index 346c0350..16e733b1 100644
--- a/features/create_sites.feature
+++ b/features/create_sites.feature
@@ -117,3 +117,14 @@ Feature: Create sites
     When I run jekyll
     Then the _site directory should exist
     And I should see "SomeDirective" in "_site/.htaccess"
+
+  Scenario: File was replaced by a directory
+    Given I have a "test" file that contains "some stuff"
+    When I run jekyll
+    Then the _site directory should exist
+    When I delete the file "test"
+    Given I have a test directory
+    And I have a "test/index.html" file that contains "some other stuff"
+    When I run jekyll
+    Then the _site/test directory should exist
+    And I should see "some other stuff" in "_site/test/index.html"
diff --git a/features/step_definitions/jekyll_steps.rb b/features/step_definitions/jekyll_steps.rb
index c1f4347f..1dca32d9 100644
--- a/features/step_definitions/jekyll_steps.rb
+++ b/features/step_definitions/jekyll_steps.rb
@@ -131,6 +131,10 @@ When /^I change "(.*)" to contain "(.*)"$/ do |file, text|
   end
 end
 
+When /^I delete the file "(.*)"$/ do |file|
+  File.delete(file)
+end
+
 Then /^the (.*) directory should exist$/ do |dir|
   assert File.directory?(dir), "The directory \"#{dir}\" does not exist"
 end
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index e1eb95e2..e8990b85 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -270,7 +270,11 @@ module Jekyll
       files.each { |file| dirs << File.dirname(file) }
       files.merge(dirs)
 
-      obsolete_files = dest_files - files
+      # files that are replaced by dirs should be deleted
+      files_to_delete = Set.new
+      dirs.each { |dir| files_to_delete << dir if File.file?(dir) }
+
+      obsolete_files = dest_files - files + files_to_delete
       FileUtils.rm_rf(obsolete_files.to_a)
     end