diff --git a/lib/kintsugi/apply_change_to_project.rb b/lib/kintsugi/apply_change_to_project.rb
index 403e307..82657c9 100644
--- a/lib/kintsugi/apply_change_to_project.rb
+++ b/lib/kintsugi/apply_change_to_project.rb
@@ -309,8 +309,21 @@ def add_child_to_component(component, change)
     def add_reference_proxy(containing_component, change)
       case containing_component
       when Xcodeproj::Project::PBXBuildFile
-        containing_component.file_ref = find_reference_proxy(containing_component.project,
-                                                             change["remoteRef"])
+        # If there are two file references that refer to the same file, one with a build file and
+        # the other one without, this method will prefer to take the one without the build file.
+        # This assumes that it's preferred to have a file reference with build file than a file
+        # reference without/with two build files.
+        filter_files_without_build_files = lambda do |reference|
+          reference.referrers.find do |referrer|
+            referrer.is_a?(Xcodeproj::Project::PBXBuildFile)
+          end.nil?
+        end
+        file_reference = find_reference_proxy(containing_component.project, change["remoteRef"],
+                                              reference_filter: filter_files_without_build_files)
+        if file_reference.nil?
+          file_reference = find_reference_proxy(containing_component.project, change["remoteRef"])
+        end
+        containing_component.file_ref = file_reference
       when Xcodeproj::Project::PBXGroup
         reference_proxy = containing_component.project.new(Xcodeproj::Project::PBXReferenceProxy)
         containing_component << reference_proxy
@@ -469,7 +482,7 @@ def add_subproject_reference(root_object, project_reference_change)
       end
       subproject_reference =
         find_file(root_object.project, project_reference_change["ProjectRef"],
-                  filter_file: filter_subproject_without_project_references)
+                  file_filter: filter_subproject_without_project_references)
 
       attribute =
         Xcodeproj::Project::PBXProject.references_by_keys_attributes
@@ -572,10 +585,9 @@ def add_attributes_to_component(component, change, ignore_keys: [])
       end
     end
 
-    def find_file(project, file_reference_change, filter_file: ->(_) { true })
+    def find_file(project, file_reference_change, file_filter: ->(_) { true })
       file_references = project.files.select do |file_reference|
-        next file_reference.path == file_reference_change["path"] &&
-          filter_file.call(file_reference)
+        file_reference.path == file_reference_change["path"] && file_filter.call(file_reference)
       end
       if file_references.length > 1
         puts "Debug: Found more than one matching file with path " \
@@ -589,12 +601,13 @@ def find_file(project, file_reference_change, filter_file: ->(_) { true })
       file_references.first
     end
 
-    def find_reference_proxy(project, container_item_proxy_change)
+    def find_reference_proxy(project, container_item_proxy_change, reference_filter: ->(_) { true })
       reference_proxies = project.root_object.project_references.map do |project_ref_and_products|
         project_ref_and_products[:product_group].children.find do |product|
           product.remote_ref.remote_global_id_string ==
             container_item_proxy_change["remoteGlobalIDString"] &&
-            product.remote_ref.remote_info == container_item_proxy_change["remoteInfo"]
+            product.remote_ref.remote_info == container_item_proxy_change["remoteInfo"] &&
+            reference_filter.call(product)
         end
       end.compact
 
diff --git a/spec/kintsugi_apply_change_to_project_spec.rb b/spec/kintsugi_apply_change_to_project_spec.rb
index f9faebf..f38b4c9 100644
--- a/spec/kintsugi_apply_change_to_project_spec.rb
+++ b/spec/kintsugi_apply_change_to_project_spec.rb
@@ -449,6 +449,30 @@
       expect(base_project).to be_equivalent_to_project(theirs_project, ignore_keys: ["containerPortal"])
     end
 
+    it "adds build file to a file reference that already exist" do
+      file_reference = base_project.main_group.new_reference("bar")
+      base_project.targets[0].frameworks_build_phase.add_file_reference(file_reference)
+
+      base_project.main_group.new_reference("bar")
+
+      base_project.save
+
+      theirs_project = create_copy_of_project(base_project.path, "theirs")
+
+      theirs_file_reference = theirs_project.main_group.files.find do |file|
+        !file.referrers.find { |referrer| referrer.is_a?(Xcodeproj::Project::PBXBuildFile) } &&
+          file.display_name == "bar"
+      end
+      theirs_project.targets[0].frameworks_build_phase.add_file_reference(theirs_file_reference)
+
+      changes_to_apply = get_diff(theirs_project, base_project)
+
+      described_class.apply_change_to_project(base_project, changes_to_apply)
+      base_project.save
+
+      expect(base_project).to be_equivalent_to_project(theirs_project)
+    end
+
     it "adds file reference to build file" do
       file_reference = base_project.main_group.new_reference("bar")