diff --git a/app/jobs/scheduled/clean_up_uploads.rb b/app/jobs/scheduled/clean_up_uploads.rb
index 21f67f81f30..07aef08d580 100644
--- a/app/jobs/scheduled/clean_up_uploads.rb
+++ b/app/jobs/scheduled/clean_up_uploads.rb
@@ -5,31 +5,29 @@ module Jobs
     def execute(args)
       return unless SiteSetting.clean_up_uploads?
 
-      ignore_urls  = []
-      ignore_urls |= UserProfile.uniq.where("profile_background IS NOT NULL AND profile_background != ''").pluck(:profile_background)
-      ignore_urls |= UserProfile.uniq.where("card_background IS NOT NULL AND card_background != ''").pluck(:card_background)
-      ignore_urls |= Category.uniq.where("logo_url IS NOT NULL AND logo_url != ''").pluck(:logo_url)
-      ignore_urls |= Category.uniq.where("background_url IS NOT NULL AND background_url != ''").pluck(:background_url)
-
       # Any URLs in site settings are fair game
-      ignore_urls |= [
+      ignore_urls = [
         SiteSetting.logo_url,
         SiteSetting.logo_small_url,
         SiteSetting.favicon_url,
         SiteSetting.apple_touch_icon_url
       ]
 
-      ids  = []
-      ids |= PostUpload.uniq.pluck(:upload_id)
-      ids |= User.uniq.where("uploaded_avatar_id IS NOT NULL").pluck(:uploaded_avatar_id)
-      ids |= UserAvatar.uniq.where("gravatar_upload_id IS NOT NULL").pluck(:gravatar_upload_id)
-
       grace_period = [SiteSetting.clean_orphan_uploads_grace_period_hours, 1].max
 
-      result = Upload.where("retain_hours IS NULL OR created_at < current_timestamp - interval '1 hour' * retain_hours")
-      result = result.where("created_at < ?", grace_period.hour.ago)
-      result = result.where("id NOT IN (?)", ids) if !ids.empty?
-      result = result.where("url NOT IN (?)", ignore_urls) if !ignore_urls.empty?
+      result = Upload.where("uploads.retain_hours IS NULL OR uploads.created_at < current_timestamp - interval '1 hour' * uploads.retain_hours")
+        .where("uploads.created_at < ?", grace_period.hour.ago)
+        .joins("LEFT JOIN post_uploads pu ON pu.upload_id = uploads.id")
+        .joins("LEFT JOIN users u ON u.uploaded_avatar_id = uploads.id")
+        .joins("LEFT JOIN user_avatars ua ON (ua.gravatar_upload_id = uploads.id OR ua.custom_upload_id = uploads.id)")
+        .joins("LEFT JOIN user_profiles up ON up.profile_background = uploads.url OR up.card_background = uploads.url")
+        .joins("LEFT JOIN categories c ON c.logo_url = uploads.url OR c.background_url = uploads.url")
+        .where("pu.upload_id IS NULL")
+        .where("u.uploaded_avatar_id IS NULL")
+        .where("ua.gravatar_upload_id IS NULL AND ua.custom_upload_id IS NULL")
+        .where("up.profile_background IS NULL AND up.card_background IS NULL")
+        .where("c.logo_url IS NULL AND c.background_url IS NULL")
+        .where("uploads.url NOT IN (?)", ignore_urls)
 
       result.find_each do |upload|
         next if QueuedPost.where("raw LIKE '%#{upload.sha1}%'").exists?
diff --git a/db/migrate/20161102024700_add_post_uploads_indexes.rb b/db/migrate/20161102024700_add_post_uploads_indexes.rb
new file mode 100644
index 00000000000..c8f8ced7143
--- /dev/null
+++ b/db/migrate/20161102024700_add_post_uploads_indexes.rb
@@ -0,0 +1,6 @@
+class AddPostUploadsIndexes < ActiveRecord::Migration
+  def change
+    add_index :post_uploads, :post_id
+    add_index :post_uploads, :upload_id
+  end
+end
diff --git a/db/migrate/20161102024818_add_uploaded_avatar_id_index_to_users.rb b/db/migrate/20161102024818_add_uploaded_avatar_id_index_to_users.rb
new file mode 100644
index 00000000000..2e5c6e66e17
--- /dev/null
+++ b/db/migrate/20161102024818_add_uploaded_avatar_id_index_to_users.rb
@@ -0,0 +1,5 @@
+class AddUploadedAvatarIdIndexToUsers < ActiveRecord::Migration
+  def change
+    add_index :users, :uploaded_avatar_id
+  end
+end
diff --git a/db/migrate/20161102024838_add_user_avatars_indexes.rb b/db/migrate/20161102024838_add_user_avatars_indexes.rb
new file mode 100644
index 00000000000..ea1b26f7f78
--- /dev/null
+++ b/db/migrate/20161102024838_add_user_avatars_indexes.rb
@@ -0,0 +1,6 @@
+class AddUserAvatarsIndexes < ActiveRecord::Migration
+  def change
+    add_index :user_avatars, :custom_upload_id
+    add_index :user_avatars, :gravatar_upload_id
+  end
+end
diff --git a/db/migrate/20161102024900_add_user_profiles_indexes.rb b/db/migrate/20161102024900_add_user_profiles_indexes.rb
new file mode 100644
index 00000000000..7a5ce85f26d
--- /dev/null
+++ b/db/migrate/20161102024900_add_user_profiles_indexes.rb
@@ -0,0 +1,6 @@
+class AddUserProfilesIndexes < ActiveRecord::Migration
+  def change
+    add_index :user_profiles, :profile_background
+    add_index :user_profiles, :card_background
+  end
+end
diff --git a/db/migrate/20161102024920_add_categories_indexes.rb b/db/migrate/20161102024920_add_categories_indexes.rb
new file mode 100644
index 00000000000..d5ad88f10d9
--- /dev/null
+++ b/db/migrate/20161102024920_add_categories_indexes.rb
@@ -0,0 +1,6 @@
+class AddCategoriesIndexes < ActiveRecord::Migration
+  def change
+    add_index :categories, :logo_url
+    add_index :categories, :background_url
+  end
+end
diff --git a/spec/jobs/clean_up_uploads_spec.rb b/spec/jobs/clean_up_uploads_spec.rb
index 4341ec728ed..6e7c77cfc33 100644
--- a/spec/jobs/clean_up_uploads_spec.rb
+++ b/spec/jobs/clean_up_uploads_spec.rb
@@ -103,6 +103,16 @@ describe Jobs::CleanUpUploads do
     expect(Upload.find_by(id: upload.id)).to eq(upload)
   end
 
+  it "does not delete user custom upload" do
+    upload = fabricate_upload
+    Fabricate(:user, user_avatar: Fabricate(:user_avatar, custom_upload: upload))
+
+    Jobs::CleanUpUploads.new.execute(nil)
+
+    expect(Upload.find_by(id: @upload.id)).to eq(nil)
+    expect(Upload.find_by(id: upload.id)).to eq(upload)
+  end
+
   it "does not delete uploads in a queued post" do
     upload = fabricate_upload