diff --git a/NEWS.md b/NEWS.md
index bf49b0358f0711..6c748e874d314d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -88,7 +88,9 @@ releases.
 
 ### The following bundled gems are updated.
 
-* minitest 6.0.3
+* minitest 6.0.4
+* rake 13.4.1
+  * 13.3.1 to [v13.4.0][rake-v13.4.0], [v13.4.1][rake-v13.4.1]
 * test-unit 3.7.7
   * 3.7.5 to [3.7.6][test-unit-3.7.6], [3.7.7][test-unit-3.7.7]
 * net-imap 0.6.3
@@ -182,6 +184,8 @@ A lot of work has gone into making Ractors more stable, performant, and usable.
 [resolv-v0.7.1]: https://github.com/ruby/resolv/releases/tag/v0.7.1
 [strscan-v3.1.7]: https://github.com/ruby/strscan/releases/tag/v3.1.7
 [timeout-v0.6.1]: https://github.com/ruby/timeout/releases/tag/v0.6.1
+[rake-v13.4.0]: https://github.com/ruby/rake/releases/tag/v13.4.0
+[rake-v13.4.1]: https://github.com/ruby/rake/releases/tag/v13.4.1
 [test-unit-3.7.6]: https://github.com/test-unit/test-unit/releases/tag/3.7.6
 [test-unit-3.7.7]: https://github.com/test-unit/test-unit/releases/tag/3.7.7
 [net-imap-v0.6.3]: https://github.com/ruby/net-imap/releases/tag/v0.6.3
diff --git a/gems/bundled_gems b/gems/bundled_gems
index eb2ffd37f2c976..dcabd4895b8f99 100644
--- a/gems/bundled_gems
+++ b/gems/bundled_gems
@@ -6,9 +6,9 @@
 # - revision: revision in repository-url to test
 #   if `revision` is not given, "v"+`version` or `version` will be used.
 
-minitest            6.0.3  https://github.com/minitest/minitest
+minitest            6.0.4  https://github.com/minitest/minitest
 power_assert        3.0.1   https://github.com/ruby/power_assert
-rake                13.3.1  https://github.com/ruby/rake
+rake                13.4.1  https://github.com/ruby/rake
 test-unit           3.7.7   https://github.com/test-unit/test-unit
 rexml               3.4.4   https://github.com/ruby/rexml
 rss                 0.3.2   https://github.com/ruby/rss
diff --git a/lib/bundler/definition.rb b/lib/bundler/definition.rb
index a923a8cb20e8c4..a620475c18cf48 100644
--- a/lib/bundler/definition.rb
+++ b/lib/bundler/definition.rb
@@ -777,7 +777,25 @@ def start_resolution
     end
 
     def precompute_source_requirements_for_indirect_dependencies?
-      sources.non_global_rubygems_sources.all?(&:dependency_api_available?)
+      if sources.non_global_rubygems_sources.all?(&:dependency_api_available?)
+        true
+      else
+        non_dependency_api_warning
+        false
+      end
+    end
+
+    def non_dependency_api_warning
+      non_api_sources = sources.non_global_rubygems_sources.reject(&:dependency_api_available?)
+      non_api_source_names = non_api_sources.map {|d| "  * #{d}" }.join("\n")
+
+      msg = String.new
+      msg << "Your Gemfile contains scoped sources that don't implement a dependency API, namely:\n\n"
+      msg << non_api_source_names
+      msg << "\n\nUsing the above gem servers may result in installing unexpected gems. " \
+        "To resolve this warning, make sure you use gem servers that implement dependency APIs, " \
+        "such as gemstash or geminabox gem servers."
+      Bundler.ui.warn msg
     end
 
     def current_platform_locked?
diff --git a/spec/bundler/bundler/definition_spec.rb b/spec/bundler/bundler/definition_spec.rb
index 9524c70193ebd8..8c7d5667ac6657 100644
--- a/spec/bundler/bundler/definition_spec.rb
+++ b/spec/bundler/bundler/definition_spec.rb
@@ -289,6 +289,57 @@
     end
   end
 
+  describe "#precompute_source_requirements_for_indirect_dependencies?" do
+    before do
+      allow(Bundler::SharedHelpers).to receive(:find_gemfile) { Pathname.new("Gemfile") }
+    end
+
+    let(:sources) { Bundler::SourceList.new }
+    subject { Bundler::Definition.new(nil, [], sources, []) }
+
+    before do
+      allow(sources).to receive(:non_global_rubygems_sources).and_return(non_global_rubygems_sources)
+    end
+
+    context "when all the scoped sources implement a dependency API" do
+      let(:non_global_rubygems_sources) do
+        [
+          double("non-global-source-0", "dependency_api_available?":true, to_s:"a"),
+          double("non-global-source-1", "dependency_api_available?":true, to_s:"b"),
+        ]
+      end
+
+      it "returns true without warning" do
+        expect(subject).not_to receive(:non_dependency_api_warning)
+
+        expect(subject.send(:precompute_source_requirements_for_indirect_dependencies?)).to be_truthy
+      end
+    end
+
+    context "when some scoped sources do not implement a dependency API" do
+      let(:non_global_rubygems_sources) do
+        [
+          double("non-global-source-0", "dependency_api_available?":true, to_s:"a"),
+          double("non-global-source-1", "dependency_api_available?":false, to_s:"b"),
+          double("non-global-source-2", "dependency_api_available?":false, to_s:"c"),
+        ]
+      end
+
+      it "returns false and warns about the non-API sources" do
+        expect(Bundler.ui).to receive(:warn).with(<<-W.strip)
+Your Gemfile contains scoped sources that don't implement a dependency API, namely:
+
+  * b
+  * c
+
+Using the above gem servers may result in installing unexpected gems. To resolve this warning, make sure you use gem servers that implement dependency APIs, such as gemstash or geminabox gem servers.
+        W
+
+        expect(subject.send(:precompute_source_requirements_for_indirect_dependencies?)).to be_falsy
+      end
+    end
+  end
+
   def mock_source_list
     Class.new do
       def all_sources