diff --git a/lib/bundler/plugin.rb b/lib/bundler/plugin.rb
index e6aaa6b464..edd1900135 100644
--- a/lib/bundler/plugin.rb
+++ b/lib/bundler/plugin.rb
@@ -62,7 +62,8 @@ module Bundler
       if names.any?
         names.each do |name|
           if index.installed?(name)
-            Bundler.rm_rf(index.plugin_path(name))
+            path = index.plugin_path(name).to_s
+            Bundler.rm_rf(path) if index.installed_in_plugin_root?(name)
             index.unregister_plugin(name)
             Bundler.ui.info "Uninstalled plugin #{name}"
           else
diff --git a/lib/bundler/plugin/index.rb b/lib/bundler/plugin/index.rb
index a2d5eaa38a..c2ab8f90da 100644
--- a/lib/bundler/plugin/index.rb
+++ b/lib/bundler/plugin/index.rb
@@ -136,6 +136,14 @@ module Bundler
         @hooks[event] || []
       end
 
+      # This plugin is installed inside the .bundle/plugin directory,
+      # and thus is managed solely by Bundler
+      def installed_in_plugin_root?(name)
+        return false unless (path = installed?(name))
+
+        path.start_with?("#{Plugin.root}/")
+      end
+
       private
 
       # Reads the index file from the directory and initializes the instance
diff --git a/spec/bundler/plugins/uninstall_spec.rb b/spec/bundler/plugins/uninstall_spec.rb
index 8180241911..555c6a7002 100644
--- a/spec/bundler/plugins/uninstall_spec.rb
+++ b/spec/bundler/plugins/uninstall_spec.rb
@@ -30,6 +30,31 @@ RSpec.describe "bundler plugin uninstall" do
     plugin_should_not_be_installed("foo")
   end
 
+  it "doesn't wipe out path plugins" do
+    build_lib "path_plugin" do |s|
+      s.write "plugins.rb"
+    end
+    path = lib_path("path_plugin-1.0")
+    expect(path).to be_a_directory
+
+    allow(Bundler::SharedHelpers).to receive(:find_gemfile).and_return(bundled_app_gemfile)
+
+    install_gemfile <<-G
+      source '#{file_uri_for(gem_repo2)}'
+      plugin 'path_plugin', :path => "#{path}"
+      gem 'rack', '1.0.0'
+    G
+
+    plugin_should_be_installed("path_plugin")
+    expect(Bundler::Plugin.index.plugin_path("path_plugin")).to eq path
+
+    bundle "plugin uninstall path_plugin"
+    expect(out).to include("Uninstalled plugin path_plugin")
+    plugin_should_not_be_installed("path_plugin")
+    # the actual gem still exists though
+    expect(path).to be_a_directory
+  end
+
   describe "with --all" do
     it "uninstalls all installed plugins" do
       bundle "plugin install foo kung-foo --source #{file_uri_for(gem_repo2)}"