diff --git a/logstash-core/lib/logstash/agent.rb b/logstash-core/lib/logstash/agent.rb
index 532bf9989cc..97cdba006a8 100644
--- a/logstash-core/lib/logstash/agent.rb
+++ b/logstash-core/lib/logstash/agent.rb
@@ -22,6 +22,13 @@ class LogStash::Agent
   include LogStash::Util::Loggable
   STARTED_AT = Time.now.freeze
 
+  # Only one agent object should be active at a time
+  # This invariant is mostly here for tests, to ensure we don't accidentally start two
+  # We record the backtrace of every agent start to make it possible to locate the source
+  # of the conflict, since it will be the preceeding instantiation that is the likely leak
+  CURRENT = java.util.concurrent.atomic.AtomicReference.new
+  CURRENT_INITIALIZED_BACKTRACE = java.util.concurrent.atomic.AtomicReference.new
+
   attr_reader :metric, :name, :settings, :webserver, :dispatcher, :ephemeral_id, :pipelines, :pipeline_bus
   attr_accessor :logger
 
@@ -31,6 +38,14 @@ class LogStash::Agent
   #   :auto_reload [Boolean] - enable reloading of pipelines
   #   :reload_interval [Integer] - reload pipelines every X seconds
   def initialize(settings = LogStash::SETTINGS, source_loader = nil)
+
+    # Check that we are the sole live instance
+    if (CURRENT.compare_and_set(nil, self))
+      CURRENT_INITIALIZED_BACKTRACE.set(Kernel.caller);
+    else
+      raise "Only one agent may be active at a time! Cannot start a new one, old instance initialized in #{CURRENT_INITIALIZED_BACKTRACE.get.inspect}"
+    end
+
     @logger = self.class.logger
     @settings = settings
     @auto_reload = setting("config.reload.automatic")
@@ -178,6 +193,11 @@ def shutdown
     transition_to_stopped
     converge_result = shutdown_pipelines
     converge_result
+
+    # Allow other agents to be created again
+    if (!CURRENT.compare_and_set(self, nil))
+      raise "Current agent is not the one that is shutting down, #{CURRENT.get.object_id} should be shut down. This should never happen"
+    end
   end
 
   def id
diff --git a/logstash-core/spec/logstash/agent_spec.rb b/logstash-core/spec/logstash/agent_spec.rb
index 6588347ae7b..a23501252ac 100644
--- a/logstash-core/spec/logstash/agent_spec.rb
+++ b/logstash-core/spec/logstash/agent_spec.rb
@@ -50,11 +50,8 @@
   end
 
   after :each do
-    subject.shutdown
-    LogStash::SETTINGS.reset
-
     FileUtils.rm(config_file)
-    FileUtils.rm_rf(subject.id_path)
+    LogStash::SETTINGS.reset
   end
 
   it "fallback to hostname when no name is provided" do
@@ -120,7 +117,6 @@
 
           Stud.stop!(t)
           t.join
-          subject.shutdown
         end
       end
 
@@ -141,7 +137,6 @@
 
             Stud.stop!(t)
             t.join
-            subject.shutdown
           end
         end
 
@@ -162,7 +157,6 @@
 
             Stud.stop!(t)
             t.join
-            subject.shutdown
           end
         end
 
@@ -185,7 +179,6 @@
 
             Stud.stop!(t)
             t.join
-            subject.shutdown
           end
         end
 
@@ -206,7 +199,6 @@
 
             Stud.stop!(t)
             t.join
-            subject.shutdown
           end
         end
       end
@@ -229,10 +221,6 @@
 
     subject { described_class.new(mock_settings(agent_args), source_loader) }
 
-    after do
-      subject.shutdown
-    end
-
     context "environment variable templating" do
       before :each do
         @foo_content = ENV["FOO"]
@@ -273,18 +261,13 @@
       expect(subject.converge_state_and_update).to be_a_successful_converge
     end
 
-    after(:each) do
-      # new pipelines will be created part of the upgrade process so we need
-      # to close any initialized pipelines
-      subject.shutdown
-    end
-
     context "when the upgrade fails" do
       it "leaves the state untouched" do
         expect(subject.converge_state_and_update).not_to be_a_successful_converge
         expect(subject.get_pipeline(default_pipeline_id).config_str).to eq(pipeline_config)
       end
 
+
       # TODO(ph): This valid?
       xcontext "and current state is empty" do
         it "should not start a pipeline" do
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index 30ab077c047..313ad0ba314 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -52,6 +52,17 @@ def puts(payload)
       example.run
     end
   end
+
+  c.after(:each) do
+    # Sometime tests instantiate an agent but don't shut it down
+    # We conveniently handle this, to prevent tests from polluting each other
+    current_agent = ::LogStash::Agent::CURRENT.get
+    if current_agent
+      current_agent.shutdown
+
+      FileUtils.rm_rf(current_agent.id_path)
+    end
+  end
 end
 
 def installed_plugins