diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/BuiltinTypesTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/BuiltinTypesTest.scala
index 939b2469ec65..883f8481ec14 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/BuiltinTypesTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/BuiltinTypesTest.scala
@@ -97,6 +97,10 @@ class BuiltinTypesTest
     context = new TestContext("Test")
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
 
   def runCode(contextId: UUID, requestId: UUID, contents: String): Unit = {
     val moduleName = "Enso_Test.Test.Main"
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeAsyncCommandsTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeAsyncCommandsTest.scala
index 6b2a181a0f50..d6bc7938fb5b 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeAsyncCommandsTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeAsyncCommandsTest.scala
@@ -100,6 +100,10 @@ class RuntimeAsyncCommandsTest
     context = new TestContext("Test")
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
 
   it should "interrupt stopped execution context" in {
     val moduleName = "Enso_Test.Test.Main"
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeComponentsTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeComponentsTest.scala
index 16762ff826d1..1b5631a451a6 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeComponentsTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeComponentsTest.scala
@@ -200,6 +200,10 @@ class RuntimeComponentsTest
     context = new TestContext("Test")
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
 
   it should "load library extended by the component group" in {
     val contextId  = UUID.randomUUID()
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala
index 0c8b7426f16b..a1adcf638198 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala
@@ -106,6 +106,11 @@ class RuntimeErrorsTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   it should "return panic sentinels in method body" in {
     val contextId  = UUID.randomUUID()
     val requestId  = UUID.randomUUID()
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeExecutionEnvironmentTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeExecutionEnvironmentTest.scala
index 1bf6964e20b9..86dfe961431a 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeExecutionEnvironmentTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeExecutionEnvironmentTest.scala
@@ -129,6 +129,11 @@ class RuntimeExecutionEnvironmentTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   it should "panic when output context is not enabled" in {
 
     val contextId  = UUID.randomUUID()
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala
index 8a849afe5772..3f682e1be449 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala
@@ -99,6 +99,11 @@ class RuntimeInstrumentTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   it should "instrument simple expression" in {
     val contextId  = UUID.randomUUID()
     val requestId  = UUID.randomUUID()
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
index dd3d4d19fa40..85812546b1a3 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
@@ -331,6 +331,11 @@ class RuntimeServerTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   "RuntimeServer" should "push and pop functions on the stack" in {
     val contents  = context.Main.code
     val mainFile  = context.writeMain(contents)
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala
index 387fd662ce9a..baf046d87e30 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala
@@ -185,6 +185,11 @@ class RuntimeStdlibTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   it should "import Base modules" in {
     val contextId  = UUID.randomUUID()
     val requestId  = UUID.randomUUID()
diff --git a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala
index 7021f0fde9b2..b6aa4accea96 100644
--- a/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala
+++ b/engine/runtime-with-instruments/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala
@@ -94,6 +94,11 @@ class RuntimeSuggestionUpdatesTest
     val Some(Api.Response(_, Api.InitializedNotification())) = context.receive
   }
 
+  override protected def afterEach(): Unit = {
+    context.executionContext.context.close()
+    context.runtimeServerEmulator.terminate()
+  }
+
   it should "send suggestion updates after file modification" in {
     val contextId  = UUID.randomUUID()
     val requestId  = UUID.randomUUID()
diff --git a/engine/runtime/src/main/java/org/enso/interpreter/runtime/ThreadExecutors.java b/engine/runtime/src/main/java/org/enso/interpreter/runtime/ThreadExecutors.java
index 0484c80ed8eb..394e4e4aa0e6 100644
--- a/engine/runtime/src/main/java/org/enso/interpreter/runtime/ThreadExecutors.java
+++ b/engine/runtime/src/main/java/org/enso/interpreter/runtime/ThreadExecutors.java
@@ -5,7 +5,9 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.ThreadFactory;
+import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.logging.Level;
 
 final class ThreadExecutors {
   private final EnsoContext context;
@@ -32,6 +34,17 @@ public void shutdown() {
     while (it.hasNext()) {
       var p = it.next().getKey();
       p.shutdown();
+      boolean success;
+      try {
+        success = p.awaitTermination(10, TimeUnit.SECONDS);
+      } catch (InterruptedException ex) {
+        success = false;
+      }
+      if (!success) {
+        context
+            .getLogger()
+            .log(Level.WARNING, "Cannot shutdown {0} thread pool", it.next().getValue());
+      }
     }
   }
 
diff --git a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/execution/JobExecutionEngine.scala b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/execution/JobExecutionEngine.scala
index e36953b1ec0c..97344df3ba10 100644
--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/execution/JobExecutionEngine.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/execution/JobExecutionEngine.scala
@@ -175,6 +175,7 @@ final class JobExecutionEngine(
     runtimeContext.executionService.getContext.getThreadManager
       .interruptThreads()
     jobExecutor.shutdownNow()
+    backgroundJobExecutor.shutdownNow()
   }
 
   /** Submit background jobs preserving the stable order. */
diff --git a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerEmulator.scala b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerEmulator.scala
index cea4fece68c4..710f68de64a4 100644
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerEmulator.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerEmulator.scala
@@ -80,4 +80,6 @@ class RuntimeServerEmulator(
       }
     } else null
   }
+
+  def terminate() = system.terminate()
 }