diff --git a/bundler/lib/bundler.rb b/bundler/lib/bundler.rb
index f6ad7ccaef84..0ddd2c7f8804 100644
--- a/bundler/lib/bundler.rb
+++ b/bundler/lib/bundler.rb
@@ -602,6 +602,10 @@ def reset!
       reset_rubygems!
     end
 
+    def reset_settings!
+      @settings = nil
+    end
+
     def reset_paths!
       @bin_path = nil
       @bundler_major_version = nil
diff --git a/bundler/lib/bundler/cli.rb b/bundler/lib/bundler/cli.rb
index c0e3802bc9aa..e2dceb98d5fa 100644
--- a/bundler/lib/bundler/cli.rb
+++ b/bundler/lib/bundler/cli.rb
@@ -57,7 +57,7 @@ def initialize(*args)
       custom_gemfile = options[:gemfile] || Bundler.settings[:gemfile]
       if custom_gemfile && !custom_gemfile.empty?
         Bundler::SharedHelpers.set_env "BUNDLE_GEMFILE", File.expand_path(custom_gemfile)
-        Bundler.reset_paths!
+        Bundler.reset_settings!
       end
 
       Bundler.settings.set_command_option_if_given :retry, options[:retry]
diff --git a/bundler/spec/commands/exec_spec.rb b/bundler/spec/commands/exec_spec.rb
index 074eb5ef8353..b1c5a2e5bc66 100644
--- a/bundler/spec/commands/exec_spec.rb
+++ b/bundler/spec/commands/exec_spec.rb
@@ -865,6 +865,8 @@ def bin_path(a,b,c)
   context "nested bundle exec" do
     context "when bundle in a local path" do
       before do
+        skip "https://github.com/rubygems/rubygems/issues/3351" if Gem.win_platform?
+
         gemfile <<-G
           source "#{file_uri_for(gem_repo1)}"
           gem "rack"
@@ -874,8 +876,6 @@ def bin_path(a,b,c)
       end
 
       it "correctly shells out" do
-        skip "https://github.com/rubygems/rubygems/issues/3351" if Gem.win_platform?
-
         file = bundled_app("file_that_bundle_execs.rb")
         create_file(file, <<-RUBY)
           #!#{Gem.ruby}
@@ -887,6 +887,49 @@ def bin_path(a,b,c)
       end
     end
 
+    context "when Kernel.require uses extra monkeypatches" do
+      before do
+        skip "https://github.com/rubygems/rubygems/issues/3351" if Gem.win_platform?
+
+        install_gemfile ""
+      end
+
+      it "does not undo the monkeypatches" do
+        karafka = bundled_app("bin/karafka")
+        create_file(karafka, <<~RUBY)
+          #!#{Gem.ruby}
+
+          module Kernel
+            module_function
+
+            alias_method :require_before_extra_monkeypatches, :require
+
+            def require(path)
+              puts "requiring \#{path} used the monkeypatch"
+
+              require_before_extra_monkeypatches(path)
+            end
+          end
+
+          Bundler.setup(:default)
+
+          require "foo"
+        RUBY
+        karafka.chmod(0o777)
+
+        foreman = bundled_app("bin/foreman")
+        create_file(foreman, <<~RUBY)
+          #!#{Gem.ruby}
+
+          puts `bundle exec bin/karafka`
+        RUBY
+        foreman.chmod(0o777)
+
+        bundle "exec #{foreman}"
+        expect(out).to eq("requiring foo used the monkeypatch")
+      end
+    end
+
     context "with a system gem that shadows a default gem" do
       let(:openssl_version) { "99.9.9" }
       let(:expected) { ruby "gem 'openssl', '< 999999'; require 'openssl'; puts OpenSSL::VERSION", :artifice => nil, :raise_on_error => false }