diff --git a/Library/Homebrew/diagnostic.rb b/Library/Homebrew/diagnostic.rb
index c14bbaeb74..b039069da9 100644
--- a/Library/Homebrew/diagnostic.rb
+++ b/Library/Homebrew/diagnostic.rb
@@ -835,7 +835,14 @@ module Homebrew
         kegs = Keg.all
 
         deleted_formulae = kegs.map do |keg|
-          next if Formulary::FromNameLoader.try_new(keg.name, warn: false).nil?
+          next if Formulary.tap_paths(keg.name).any?
+
+          unless EnvConfig.no_install_from_api?
+            # Formulae installed from the API should not count as deleted formulae
+            # but may not have a tap listed in their tab
+            tap = Tab.for_keg(keg).tap
+            next if (tap.blank? || tap.core_tap?) && Homebrew::API::Formula.all_formulae.key?(keg.name)
+          end
 
           keg.name
         end.compact.uniq
diff --git a/Library/Homebrew/formulary.rb b/Library/Homebrew/formulary.rb
index 49822652b9..015e94d22f 100644
--- a/Library/Homebrew/formulary.rb
+++ b/Library/Homebrew/formulary.rb
@@ -1172,6 +1172,18 @@ module Formulary
     find_formula_in_tap(name.to_s.downcase, CoreTap.instance)
   end
 
+  def self.tap_paths(name)
+    name = name.to_s.downcase
+    Tap.map do |tap|
+      formula_path = find_formula_in_tap(name, tap)
+
+      alias_path = tap.alias_dir/name
+      next alias_path if !formula_path.exist? && alias_path.exist?
+
+      formula_path
+    end.select(&:file?)
+  end
+
   sig { params(name: String, tap: Tap).returns(Pathname) }
   def self.find_formula_in_tap(name, tap)
     filename = if name.end_with?(".rb")