diff --git a/lib/bundle/commands/cleanup.rb b/lib/bundle/commands/cleanup.rb
index 1e82149ed5..cdb9d81ea0 100644
--- a/lib/bundle/commands/cleanup.rb
+++ b/lib/bundle/commands/cleanup.rb
@@ -145,7 +145,9 @@ def recursive_dependencies(current_formulae, formulae_names, top_level: true)
 
       def taps_to_untap(global: false, file: nil)
         @dsl ||= Brewfile.read(global:, file:)
+        kept_formulae = @dsl.entries.select { |e| e.type == :brew }.map(&:name).map(&Formulary.method(:factory))
         kept_taps = @dsl.entries.select { |e| e.type == :tap }.map(&:name)
+        kept_taps += kept_formulae.filter_map(&:tap).map(&:name)
         current_taps = Bundle::TapDumper.tap_names
         current_taps - kept_taps - IGNORED_TAPS
       end