diff --git a/build.gradle b/build.gradle
index bf7e8ae6577..8f71db36f9c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -425,6 +425,7 @@ project(":logstash-core") {
     tasks.getByPath(":logstash-core:" + tsk).configure {
       dependsOn copyPluginTestAlias
       dependsOn installDevelopmentGems
+      dependsOn installDefaultGems
     }
   }
 }
@@ -1008,6 +1009,7 @@ if (System.getenv('OSS') != 'true') {
     ["rubyTests", "rubyIntegrationTests", "test"].each { tsk ->
       tasks.getByPath(":logstash-xpack:" + tsk).configure {
         dependsOn installDevelopmentGems
+        dependsOn installDefaultGems
       }
     }
   }
diff --git a/lib/bootstrap/rspec.rb b/lib/bootstrap/rspec.rb
index 782455135ee..db6cdeb7571 100755
--- a/lib/bootstrap/rspec.rb
+++ b/lib/bootstrap/rspec.rb
@@ -17,6 +17,16 @@
 
 require_relative "environment"
 LogStash::Bundler.setup!({:without => [:build]})
+# Our use of LogStash::Bundler.setup! here leaves us in kind of a wonky state for *all* tests
+# Essentially we end up with a load path that favors bundlers gem env over stdlib. This is
+# not really the call stack in logstash itself, so while this does make the full bundled gem
+# env available for tests, it also has a quirk where stdlib gems are not loaed correctly. The
+# following patch ensures that stdlib gems are bumped to the front of the load path for unit
+# tests.
+## START PATCH ##
+jruby_stdlib = $LOAD_PATH.find { |p| p.end_with?('vendor/jruby/lib/ruby/stdlib') }
+$LOAD_PATH.unshift($LOAD_PATH.delete(jruby_stdlib)) if jruby_stdlib
+## END PATCH ##
 require "logstash-core"
 require "logstash/environment"
 
diff --git a/lib/pluginmanager/gem_installer.rb b/lib/pluginmanager/gem_installer.rb
index e5560a78025..17eb889ef8e 100644
--- a/lib/pluginmanager/gem_installer.rb
+++ b/lib/pluginmanager/gem_installer.rb
@@ -15,6 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
+require "bootstrap/environment"
 require "pluginmanager/ui"
 require "pathname"
 require "rubygems/package"
@@ -26,17 +27,16 @@ module LogStash module PluginManager
   # - Generate the specifications
   # - Copy the data in the right folders
   class GemInstaller
-    GEM_HOME = Pathname.new(::File.join(LogStash::Environment::BUNDLE_DIR, "jruby", "3.1.0"))
     SPECIFICATIONS_DIR = "specifications"
     GEMS_DIR = "gems"
     CACHE_DIR = "cache"
 
     attr_reader :gem_home
 
-    def initialize(gem_file, display_post_install_message = false, gem_home = GEM_HOME)
+    def initialize(gem_file, display_post_install_message = false)
       @gem_file = gem_file
       @gem = ::Gem::Package.new(@gem_file)
-      @gem_home = Pathname.new(gem_home)
+      @gem_home = Pathname.new(LogStash::Environment.logstash_gem_home)
       @display_post_install_message = display_post_install_message
     end
 
@@ -48,8 +48,8 @@ def install
       post_install_message
     end
 
-    def self.install(gem_file, display_post_install_message = false, gem_home = GEM_HOME)
-      self.new(gem_file, display_post_install_message, gem_home).install
+    def self.install(gem_file, display_post_install_message = false)
+      self.new(gem_file, display_post_install_message).install
     end
 
     private
diff --git a/rakelib/artifacts.rake b/rakelib/artifacts.rake
index 248553b2708..2616096dd60 100644
--- a/rakelib/artifacts.rake
+++ b/rakelib/artifacts.rake
@@ -101,18 +101,6 @@ namespace "artifact" do
     @exclude_paths << 'vendor/**/gems/**/Gemfile.lock'
     @exclude_paths << 'vendor/**/gems/**/Gemfile'
 
-    @exclude_paths << 'vendor/jruby/lib/ruby/gems/shared/gems/rake-*'
-    # exclude ruby-maven-libs 3.3.9 jars until JRuby ships with >= 3.8.9
-    @exclude_paths << 'vendor/bundle/jruby/**/gems/ruby-maven-libs-3.3.9/**/*'
-
-    # remove this after JRuby includes rexml 3.3.x
-    @exclude_paths << 'vendor/jruby/lib/ruby/gems/shared/gems/rexml-3.2.5/**/*'
-    @exclude_paths << 'vendor/jruby/lib/ruby/gems/shared/specifications/rexml-3.2.5.gemspec'
-
-    # remove this after JRuby includes net-imap-0.2.4+
-    @exclude_paths << 'vendor/jruby/lib/ruby/gems/shared/specifications/net-imap-0.2.3.gemspec'
-    @exclude_paths << 'vendor/jruby/lib/ruby/gems/shared/gems/net-imap-0.2.3/**/*'
-
     # Exclude env2yaml source files - only compiled classes should be in tarball
     @exclude_paths << 'docker/data/logstash/env2yaml/**/*.java'
     @exclude_paths << 'docker/data/logstash/env2yaml/build.gradle'
diff --git a/rakelib/plugin.rake b/rakelib/plugin.rake
index 47d572f417a..3742b59b8d5 100644
--- a/rakelib/plugin.rake
+++ b/rakelib/plugin.rake
@@ -90,12 +90,65 @@ namespace "plugin" do
     task.reenable # Allow this task to be run again
   end # task "install"
 
+
+  task "clean-duplicate-gems" do
+    shared_gems_path = File.join(LogStash::Environment::LOGSTASH_HOME,
+                                  'vendor/jruby/lib/ruby/gems/shared/gems')
+    default_gemspecs_path = File.join(LogStash::Environment::LOGSTASH_HOME,
+                                       'vendor/jruby/lib/ruby/gems/shared/specifications/default')
+    bundle_gems_path = File.join(LogStash::Environment::BUNDLE_DIR,
+                                  'jruby/*/gems')
+
+    # "bundled" gems in jruby
+    # https://github.com/jruby/jruby/blob/024123c29d73b672d50730117494f3e4336a0edb/lib/pom.rb#L108-L152
+    shared_gem_names = Dir.glob(File.join(shared_gems_path, '*')).map do |path|
+      match = File.basename(path).match(/^(.+?)-\d+/)
+      match ? match[1] : nil
+    end.compact
+
+    # "default" gems in jruby/ruby
+    # https://github.com/jruby/jruby/blob/024123c29d73b672d50730117494f3e4336a0edb/lib/pom.rb#L21-L106
+    default_gem_names = Dir.glob(File.join(default_gemspecs_path, '*.gemspec')).map do |path|
+      match = File.basename(path).match(/^(.+?)-\d+/)
+      match ? match[1] : nil
+    end.compact
+
+    # gems we explicitly manage with bundler (we always want these to take precedence)
+    bundle_gem_names = Dir.glob(File.join(bundle_gems_path, '*')).map do |path|
+      match = File.basename(path).match(/^(.+?)-\d+/)
+      match ? match[1] : nil
+    end.compact
+
+    shared_duplicates = shared_gem_names & bundle_gem_names
+    default_duplicates = default_gem_names & bundle_gem_names
+    all_duplicates = (shared_duplicates + default_duplicates).uniq
+
+    puts("[plugin:clean-duplicate-gems] Removing duplicate gems: #{all_duplicates.sort.join(', ')}")
+
+    # Remove shared/bundled gem duplicates
+    shared_duplicates.each do |gem_name|
+      FileUtils.rm_rf(Dir.glob("#{shared_gems_path}/#{gem_name}-*"))
+      FileUtils.rm_rf(Dir.glob("#{shared_gems_path}/../specifications/#{gem_name}-*.gemspec"))
+    end
+
+    # Remove default gem gemspecs only
+    default_duplicates.each do |gem_name|
+      # For stdlib default gems we only remove the gemspecs as removing the source code 
+      # files results in code loading errors and ruby warnings
+      FileUtils.rm_rf(Dir.glob("#{default_gemspecs_path}/#{gem_name}-*.gemspec"))
+    end
+    
+    task.reenable
+  end
+
   task "install-default" => "bootstrap" do
     puts("[plugin:install-default] Installing default plugins")
 
     remove_lockfile # because we want to use the release lockfile
     install_plugins("--no-verify", "--preserve", *LogStash::RakeLib::DEFAULT_PLUGINS)
 
+    # Clean duplicates after full gem resolution
+    Rake::Task["plugin:clean-duplicate-gems"].invoke
     task.reenable # Allow this task to be run again
   end
 
diff --git a/rubyUtils.gradle b/rubyUtils.gradle
index 4e2565f72a4..99b5387b2d3 100644
--- a/rubyUtils.gradle
+++ b/rubyUtils.gradle
@@ -279,7 +279,11 @@ tasks.register("installCustomJRuby", Copy) {
     dependsOn buildCustomJRuby
     description = "Install custom built JRuby in the vendor directory"
     inputs.file(customJRubyTar)
-    outputs.dir("${projectDir}/vendor/jruby")
+    // Don't re-extract if core JRuby is already installed. This works around
+    // gem deduplication when rake calls back in to gradle.
+    onlyIf {
+        !file("${projectDir}/vendor/jruby/bin/jruby").exists()
+    }
     from tarTree(customJRubyTar == "" ? jrubyTarPath : customJRubyTar)
     eachFile { f ->
         f.path = f.path.replaceFirst("^jruby-${customJRubyVersion}", '')
@@ -294,7 +298,11 @@ tasks.register("downloadAndInstallJRuby", Copy) {
     dependsOn=[verifyFile, installCustomJRuby]
     description = "Install JRuby in the vendor directory"
     inputs.file(jrubyTarPath)
-    outputs.dir("${projectDir}/vendor/jruby")
+    // Don't re-extract if core JRuby is already installed. This works around
+    // gem deduplication when rake calls back in to gradle.
+    onlyIf {
+        !file("${projectDir}/vendor/jruby/bin/jruby").exists()
+    }
     from tarTree(downloadJRuby.dest)
     eachFile { f ->
         f.path = f.path.replaceFirst("^jruby-${jRubyVersion}", '')
diff --git a/spec/unit/plugin_manager/gem_installer_spec.rb b/spec/unit/plugin_manager/gem_installer_spec.rb
index dd85009dfff..89ee9c93a51 100644
--- a/spec/unit/plugin_manager/gem_installer_spec.rb
+++ b/spec/unit/plugin_manager/gem_installer_spec.rb
@@ -27,18 +27,27 @@
   let(:simple_gem) { ::File.join(::File.dirname(__FILE__), "..", "..", "support", "pack", "valid-pack", "logstash", "valid-pack", "#{plugin_name}.gem") }
 
   subject { described_class }
-  let(:temporary_gem_home) { p = Stud::Temporary.pathname; FileUtils.mkdir_p(p); p }
+   let(:gem_home) { LogStash::Environment.logstash_gem_home }
+   # Clean up installed gems after each test
+   after(:each) do
+     spec_file = ::File.join(gem_home, "specifications", "#{plugin_name}.gemspec")
+     FileUtils.rm_f(spec_file) if ::File.exist?(spec_file)
+     gem_dir = ::File.join(gem_home, "gems", plugin_name)
+     FileUtils.rm_rf(gem_dir) if Dir.exist?(gem_dir)
+     cache_file = ::File.join(gem_home, "cache", "#{plugin_name}.gem")
+     FileUtils.rm_f(cache_file) if ::File.exist?(cache_file)
+   end
 
   it "install the specifications in the spec dir" do
-    subject.install(simple_gem, false, temporary_gem_home)
-    spec_file = ::File.join(temporary_gem_home, "specifications", "#{plugin_name}.gemspec")
+    subject.install(simple_gem, false)
+    spec_file = ::File.join(gem_home, "specifications", "#{plugin_name}.gemspec")
     expect(::File.exist?(spec_file)).to be_truthy
     expect(::File.size(spec_file)).to be > 0
   end
 
   it "install the gem in the gems dir" do
-    subject.install(simple_gem, false, temporary_gem_home)
-    gem_dir = ::File.join(temporary_gem_home, "gems", plugin_name)
+    subject.install(simple_gem, false)
+    gem_dir = ::File.join(gem_home, "gems", plugin_name)
     expect(Dir.exist?(gem_dir)).to be_truthy
   end
 
@@ -50,13 +59,13 @@
 
       context "when we want the message" do
         it "display the message" do
-          expect(subject.install(simple_gem, true, temporary_gem_home)).to eq(message)
+          expect(subject.install(simple_gem, true)).to eq(message)
         end
       end
 
       context "when we dont want the message" do
         it "doesn't display the message" do
-          expect(subject.install(simple_gem, false, temporary_gem_home)).to be_nil
+          expect(subject.install(simple_gem, false)).to be_nil
         end
       end
     end
@@ -65,7 +74,7 @@
       context "when we don't want the message" do
         it "doesn't display the message" do
           expect(LogStash::PluginManager.ui).not_to receive(:info).with(message)
-          subject.install(simple_gem, true, temporary_gem_home)
+          subject.install(simple_gem, true)
         end
       end
     end