diff --git a/lib/rscons/cache.rb b/lib/rscons/cache.rb
index 1b36eac..343e292 100644
--- a/lib/rscons/cache.rb
+++ b/lib/rscons/cache.rb
@@ -238,11 +238,18 @@ module Rscons
     # @param options [Hash] Optional arguments.
     # @option options [Boolean] :install
     #   Whether the target is for an install operation.
+    # @option options [Boolean] :side_effect
+    #   Whether the target is a side-effect file (no checksum will be stored).
     #
     # @return [void]
     def register_build(targets, command, deps, env, options = {})
       Array(targets).each do |target|
-        target_checksum = Rscons.phony_target?(target) ? "" : calculate_checksum(target)
+        target_checksum =
+          if options[:side_effect] or Rscons.phony_target?(target)
+            ""
+          else
+            calculate_checksum(target)
+          end
         @cache["targets"][get_cache_key(target)] = {
           "command" => Digest::MD5.hexdigest(command.inspect),
           "checksum" => target_checksum,
diff --git a/lib/rscons/environment.rb b/lib/rscons/environment.rb
index ca0178f..6283143 100644
--- a/lib/rscons/environment.rb
+++ b/lib/rscons/environment.rb
@@ -620,7 +620,7 @@ module Rscons
         # Register side-effect files as build targets so that a Cache
         # clean operation will remove them.
         builder.side_effects.each do |side_effect|
-          Cache.instance.register_build(side_effect, nil, [], self)
+          Cache.instance.register_build(side_effect, nil, [], self, side_effect: true)
           @side_effects.delete(side_effect)
         end
         @build_hooks[:post].each do |build_hook_block|