diff --git a/build.sbt b/build.sbt
index d7cdc2cc4..cfce92d0b 100644
--- a/build.sbt
+++ b/build.sbt
@@ -666,6 +666,7 @@ lazy val mainProj = (project in file("main"))
       exclude[DirectMissingMethodProblem]("sbt.Defaults.allTestGroupsTask"),
       exclude[DirectMissingMethodProblem]("sbt.Plugins.topologicalSort"),
       exclude[IncompatibleMethTypeProblem]("sbt.Defaults.allTestGroupsTask"),
+      exclude[DirectMissingMethodProblem]("sbt.StandardMain.shutdownHook")
     )
   )
   .configure(
diff --git a/main/src/main/scala/sbt/Main.scala b/main/src/main/scala/sbt/Main.scala
index 32b314ed4..3d350fc64 100644
--- a/main/src/main/scala/sbt/Main.scala
+++ b/main/src/main/scala/sbt/Main.scala
@@ -98,33 +98,36 @@ final class xMain extends xsbti.AppMain {
   }
 }
 private[sbt] object xMainImpl {
-  private[sbt] def run(configuration: xsbti.AppConfiguration): xsbti.MainResult = {
-    import BasicCommandStrings.{ DashClient, DashDashClient, runEarly }
-    import BasicCommands.early
-    import BuiltinCommands.defaults
-    import sbt.internal.CommandStrings.{ BootCommand, DefaultsCommand, InitCommand }
-    import sbt.internal.client.NetworkClient
+  private[sbt] def run(configuration: xsbti.AppConfiguration): xsbti.MainResult =
+    try {
+      import BasicCommandStrings.{ DashClient, DashDashClient, runEarly }
+      import BasicCommands.early
+      import BuiltinCommands.defaults
+      import sbt.internal.CommandStrings.{ BootCommand, DefaultsCommand, InitCommand }
+      import sbt.internal.client.NetworkClient
 
-    // if we detect -Dsbt.client=true or -client, run thin client.
-    val clientModByEnv = java.lang.Boolean.getBoolean("sbt.client")
-    val userCommands = configuration.arguments.map(_.trim)
-    if (clientModByEnv || (userCommands.exists { cmd =>
+      // if we detect -Dsbt.client=true or -client, run thin client.
+      val clientModByEnv = java.lang.Boolean.getBoolean("sbt.client")
+      val userCommands = configuration.arguments.map(_.trim)
+      if (clientModByEnv || (userCommands.exists { cmd =>
+            (cmd == DashClient) || (cmd == DashDashClient)
+          })) {
+        val args = userCommands.toList filterNot { cmd =>
           (cmd == DashClient) || (cmd == DashDashClient)
-        })) {
-      val args = userCommands.toList filterNot { cmd =>
-        (cmd == DashClient) || (cmd == DashDashClient)
+        }
+        NetworkClient.run(configuration, args)
+        Exit(0)
+      } else {
+        val state = StandardMain.initialState(
+          configuration,
+          Seq(defaults, early),
+          runEarly(DefaultsCommand) :: runEarly(InitCommand) :: BootCommand :: Nil
+        )
+        StandardMain.runManaged(state)
       }
-      NetworkClient.run(configuration, args)
-      Exit(0)
-    } else {
-      val state = StandardMain.initialState(
-        configuration,
-        Seq(defaults, early),
-        runEarly(DefaultsCommand) :: runEarly(InitCommand) :: BootCommand :: Nil
-      )
-      StandardMain.runManaged(state)
+    } finally {
+      ShutdownHooks.close()
     }
-  }
 }
 
 final class ScriptMain extends xsbti.AppMain {
@@ -155,30 +158,21 @@ object StandardMain {
   import scalacache.caffeine._
   private[sbt] lazy val cache: scalacache.Cache[Any] = CaffeineCache[Any]
 
-  private[this] val closeRunnable: Runnable = () => {
+  private[this] val closeRunnable = () => {
     cache.close()(scalacache.modes.sync.mode)
     cache.close()(scalacache.modes.scalaFuture.mode(ExecutionContext.global))
     exchange.shutdown()
   }
-  private[sbt] val shutdownHook = new Thread(closeRunnable)
 
   def runManaged(s: State): xsbti.MainResult = {
     val previous = TrapExit.installManager()
     try {
       try {
-        val hooked = try {
-          Runtime.getRuntime.addShutdownHook(shutdownHook)
-          true
-        } catch {
-          case _: IllegalArgumentException => false
-        }
+        val hook = ShutdownHooks.add(closeRunnable)
         try {
           MainLoop.runLogged(s)
         } finally {
-          closeRunnable.run()
-          if (hooked) {
-            Runtime.getRuntime.removeShutdownHook(shutdownHook)
-          }
+          hook.close()
           ()
         }
       } finally DefaultBackgroundJobService.backgroundJobService.shutdown()
diff --git a/main/src/main/scala/sbt/MainLoop.scala b/main/src/main/scala/sbt/MainLoop.scala
index d2ea976be..e4d4aac28 100644
--- a/main/src/main/scala/sbt/MainLoop.scala
+++ b/main/src/main/scala/sbt/MainLoop.scala
@@ -11,6 +11,7 @@ import java.io.PrintWriter
 import java.util.Properties
 
 import jline.TerminalFactory
+import sbt.internal.ShutdownHooks
 import sbt.internal.langserver.ErrorCodes
 import sbt.internal.util.{ ErrorHandling, GlobalLogBacking }
 import sbt.io.{ IO, Using }
@@ -27,13 +28,12 @@ object MainLoop {
     // We've disabled jline shutdown hooks to prevent classloader leaks, and have been careful to always restore
     // the jline terminal in finally blocks, but hitting ctrl+c prevents finally blocks from being executed, in that
     // case the only way to restore the terminal is in a shutdown hook.
-    val shutdownHook = new Thread(() => TerminalFactory.get().restore())
+    val shutdownHook = ShutdownHooks.add(() => TerminalFactory.get().restore())
 
     try {
-      Runtime.getRuntime.addShutdownHook(shutdownHook)
       runLoggedLoop(state, state.globalLogging.backing)
     } finally {
-      Runtime.getRuntime.removeShutdownHook(shutdownHook)
+      shutdownHook.close()
       ()
     }
   }
diff --git a/main/src/main/scala/sbt/internal/LayeredClassLoader.scala b/main/src/main/scala/sbt/internal/LayeredClassLoader.scala
index a2c00de52..6ca12c6a7 100644
--- a/main/src/main/scala/sbt/internal/LayeredClassLoader.scala
+++ b/main/src/main/scala/sbt/internal/LayeredClassLoader.scala
@@ -49,12 +49,10 @@ private[sbt] class LayeredClassLoader(
 
 private[internal] object NativeLibs {
   private[this] val nativeLibs = new jutil.HashSet[File].asScala
-  Runtime.getRuntime.addShutdownHook(new Thread("sbt.internal.native-library-deletion") {
-    override def run(): Unit = {
-      nativeLibs.foreach(IO.delete)
-      IO.deleteIfEmpty(nativeLibs.map(_.getParentFile).toSet)
-      nativeLibs.clear()
-    }
+  ShutdownHooks.add(() => {
+    nativeLibs.foreach(IO.delete)
+    IO.deleteIfEmpty(nativeLibs.map(_.getParentFile).toSet)
+    nativeLibs.clear()
   })
   def addNativeLib(lib: String): Unit = {
     nativeLibs.add(new File(lib))
diff --git a/main/src/main/scala/sbt/internal/ShutdownHooks.scala b/main/src/main/scala/sbt/internal/ShutdownHooks.scala
new file mode 100644
index 000000000..eb29674d1
--- /dev/null
+++ b/main/src/main/scala/sbt/internal/ShutdownHooks.scala
@@ -0,0 +1,45 @@
+/*
+ * sbt
+ * Copyright 2011 - 2018, Lightbend, Inc.
+ * Copyright 2008 - 2010, Mark Harrah
+ * Licensed under Apache License 2.0 (see LICENSE)
+ */
+
+package sbt.internal
+
+import java.util.concurrent.ConcurrentHashMap
+import java.util.concurrent.atomic.{ AtomicBoolean, AtomicInteger }
+
+import scala.util.control.NonFatal
+
+private[sbt] object ShutdownHooks extends AutoCloseable {
+  private[this] val idGenerator = new AtomicInteger(0)
+  private[this] val hooks = new ConcurrentHashMap[Int, () => Any]
+  private[this] val ranHooks = new AtomicBoolean(false)
+  private[this] val thread = new Thread("shutdown-hooks-run-all") {
+    override def run(): Unit = runAll()
+  }
+  private[this] val runtime = Runtime.getRuntime
+  runtime.addShutdownHook(thread)
+  private[sbt] def add[R](task: () => R): AutoCloseable = {
+    val id = idGenerator.getAndIncrement()
+    hooks.put(
+      id,
+      () =>
+        try task()
+        catch {
+          case NonFatal(e) =>
+            System.err.println(s"Caught exception running shutdown hook: $e")
+            e.printStackTrace(System.err)
+        }
+    )
+    () => Option(hooks.remove(id)).foreach(_.apply())
+  }
+  private def runAll(): Unit = if (ranHooks.compareAndSet(false, true)) {
+    hooks.forEachValue(Runtime.getRuntime.availableProcessors, _.apply())
+  }
+  override def close(): Unit = {
+    runtime.removeShutdownHook(thread)
+    runAll()
+  }
+}
diff --git a/main/src/main/scala/sbt/internal/TaskTimings.scala b/main/src/main/scala/sbt/internal/TaskTimings.scala
index 6b4976194..a4b0b3184 100644
--- a/main/src/main/scala/sbt/internal/TaskTimings.scala
+++ b/main/src/main/scala/sbt/internal/TaskTimings.scala
@@ -38,9 +38,7 @@ private[sbt] final class TaskTimings(reportOnShutdown: Boolean)
 
   if (reportOnShutdown) {
     start = System.nanoTime
-    Runtime.getRuntime.addShutdownHook(new Thread {
-      override def run() = report()
-    })
+    ShutdownHooks.add(() => report())
   }
 
   override def initial(): Unit = {
diff --git a/main/src/main/scala/sbt/internal/TaskTraceEvent.scala b/main/src/main/scala/sbt/internal/TaskTraceEvent.scala
index 63c4522ea..de8b4eede 100644
--- a/main/src/main/scala/sbt/internal/TaskTraceEvent.scala
+++ b/main/src/main/scala/sbt/internal/TaskTraceEvent.scala
@@ -36,9 +36,7 @@ private[sbt] final class TaskTraceEvent
   override def stop(): Unit = ()
 
   start = System.nanoTime
-  Runtime.getRuntime.addShutdownHook(new Thread {
-    override def run() = report()
-  })
+  ShutdownHooks.add(() => report())
 
   private[this] def report() = {
     if (timings.asScala.nonEmpty) {