diff --git a/app/jobs/scheduled/clean_up_uploads.rb b/app/jobs/scheduled/clean_up_uploads.rb
index 87e4acad282..70b4a94ee32 100644
--- a/app/jobs/scheduled/clean_up_uploads.rb
+++ b/app/jobs/scheduled/clean_up_uploads.rb
@@ -5,13 +5,21 @@ module Jobs
     def execute(args)
       return unless SiteSetting.clean_up_uploads?
 
+      base_url = Discourse.store.internal? ? Discourse.store.relative_base_url : Discourse.store.absolute_base_url
+      s3_hostname = URI.parse(base_url).hostname
+      s3_cdn_hostname = URI.parse(SiteSetting.s3_cdn_url || "").hostname
+
       # Any URLs in site settings are fair game
       ignore_urls = [
         SiteSetting.logo_url,
         SiteSetting.logo_small_url,
         SiteSetting.favicon_url,
-        SiteSetting.apple_touch_icon_url
-      ]
+        SiteSetting.apple_touch_icon_url,
+      ].map do |url|
+        url = url.dup
+        url.gsub!(s3_cdn_hostname, s3_hostname) if s3_cdn_hostname.present?
+        url[base_url] && url[url.index(base_url)..-1]
+      end.compact.uniq
 
       grace_period = [SiteSetting.clean_orphan_uploads_grace_period_hours, 1].max
 
@@ -30,7 +38,8 @@ module Jobs
         .where("up.profile_background IS NULL AND up.card_background IS NULL")
         .where("c.uploaded_logo_id IS NULL AND c.uploaded_background_id IS NULL")
         .where("ce.upload_id IS NULL AND tf.upload_id IS NULL")
-        .where("uploads.url NOT IN (?)", ignore_urls)
+
+      result = result.where("uploads.url NOT IN (?)", ignore_urls) if ignore_urls.present?
 
       result.find_each do |upload|
         next if QueuedPost.where("raw LIKE '%#{upload.sha1}%'").exists?
diff --git a/spec/jobs/clean_up_uploads_spec.rb b/spec/jobs/clean_up_uploads_spec.rb
index e9f649cbe16..d04a9eda8bd 100644
--- a/spec/jobs/clean_up_uploads_spec.rb
+++ b/spec/jobs/clean_up_uploads_spec.rb
@@ -33,6 +33,18 @@ describe Jobs::CleanUpUploads do
     expect(Upload.find_by(id: logo_upload.id)).to eq(logo_upload)
   end
 
+  it "does not clean up uploads in site settings when they use the CDN" do
+    Discourse.stubs(:asset_host).returns("//my.awesome.cdn")
+
+    logo_small_upload = fabricate_upload
+    SiteSetting.logo_small_url = "#{Discourse.asset_host}#{logo_small_upload.url}"
+
+    Jobs::CleanUpUploads.new.execute(nil)
+
+    expect(Upload.find_by(id: @upload.id)).to eq(nil)
+    expect(Upload.find_by(id: logo_small_upload.id)).to eq(logo_small_upload)
+  end
+
   it "does not delete profile background uploads" do
     profile_background_upload = fabricate_upload
     UserProfile.last.update_attributes!(profile_background: profile_background_upload.url)