diff --git a/src/main/kotlin/org/jetbrains/kotlinx/jupyter/protocol.kt b/src/main/kotlin/org/jetbrains/kotlinx/jupyter/protocol.kt
index 1e5f9b106..63c583b7b 100644
--- a/src/main/kotlin/org/jetbrains/kotlinx/jupyter/protocol.kt
+++ b/src/main/kotlin/org/jetbrains/kotlinx/jupyter/protocol.kt
@@ -195,7 +195,15 @@ fun JupyterConnection.Socket.controlMessagesHandler(msg: Message, repl: ReplForJ
         is ShutdownRequest -> {
             repl?.evalOnShutdown()
             send(makeReplyMessage(msg, MessageType.SHUTDOWN_REPLY, content = msg.content))
-            exitProcess(0)
+            // exitProcess would kill the entire process that embedded the kernel
+            // Instead the controlThread will be interrupted,
+            // which will then interrupt the mainThread and make kernelServer return
+            if (repl?.isEmbedded == true) {
+                log.info("Interrupting controlThread to trigger kernel shutdown")
+                throw InterruptedException()
+            } else {
+                exitProcess(0)
+            }
         }
     }
 }
diff --git a/src/main/kotlin/org/jetbrains/kotlinx/jupyter/repl.kt b/src/main/kotlin/org/jetbrains/kotlinx/jupyter/repl.kt
index e9626d02a..c27b107e8 100644
--- a/src/main/kotlin/org/jetbrains/kotlinx/jupyter/repl.kt
+++ b/src/main/kotlin/org/jetbrains/kotlinx/jupyter/repl.kt
@@ -132,6 +132,9 @@ interface ReplForJupyter {
     val notebook: NotebookImpl
 
     val fileExtension: String
+
+    val isEmbedded: Boolean
+        get() = false
 }
 
 fun <T> ReplForJupyter.execute(callback: ExecutionCallback<T>): T {
@@ -145,7 +148,7 @@ class ReplForJupyterImpl(
     override val resolverConfig: ResolverConfig? = null,
     override val runtimeProperties: ReplRuntimeProperties = defaultRuntimeProperties,
     private val scriptReceivers: List<Any> = emptyList(),
-    private val embedded: Boolean = false,
+    override val isEmbedded: Boolean = false,
 ) : ReplForJupyter, ReplOptions, BaseKernelHost, KotlinKernelHostProvider {
 
     constructor(
@@ -262,7 +265,7 @@ class ReplForJupyterImpl(
 
     private val evaluatorConfiguration = ScriptEvaluationConfiguration {
         implicitReceivers.invoke(v = scriptReceivers)
-        if (!embedded) {
+        if (!isEmbedded) {
             jvm {
                 val filteringClassLoader = FilteringClassLoader(ClassLoader.getSystemClassLoader()) { fqn ->
                     listOf(
diff --git a/src/test/kotlin/org/jetbrains/kotlinx/jupyter/test/embeddingTest.kt b/src/test/kotlin/org/jetbrains/kotlinx/jupyter/test/embeddingTest.kt
index 8965d9d0a..d3ec6b57d 100644
--- a/src/test/kotlin/org/jetbrains/kotlinx/jupyter/test/embeddingTest.kt
+++ b/src/test/kotlin/org/jetbrains/kotlinx/jupyter/test/embeddingTest.kt
@@ -90,7 +90,7 @@ val testLibraryDefinition2 = LibraryDefinitionImpl(
 class EmbedReplTest : AbstractReplTest() {
     private val repl = run {
         val embeddedClasspath: List<File> = System.getProperty("java.class.path").split(File.pathSeparator).map(::File)
-        ReplForJupyterImpl(resolutionInfoProvider, embeddedClasspath, embedded = true)
+        ReplForJupyterImpl(resolutionInfoProvider, embeddedClasspath, isEmbedded = true)
     }
 
     @Test