diff --git a/src/engine/runtime.js b/src/engine/runtime.js
index 1f856fafa..3979b415e 100644
--- a/src/engine/runtime.js
+++ b/src/engine/runtime.js
@@ -1844,8 +1844,12 @@ class Runtime extends EventEmitter {
             }
         }
         this.targets = newTargets;
-        // Dispose all threads.
-        this.threads.forEach(thread => this._stopThread(thread));
+        // Dispose of the active thread.
+        if (this.sequencer.activeThread !== null) {
+            this._stopThread(this.sequencer.activeThread);
+        }
+        // Remove all remaining threads from executing in the next tick.
+        this.threads = [];
     }
 
     /**
diff --git a/src/engine/sequencer.js b/src/engine/sequencer.js
index 61a758f0a..54d4870a5 100644
--- a/src/engine/sequencer.js
+++ b/src/engine/sequencer.js
@@ -51,6 +51,8 @@ class Sequencer {
          * @type {!Runtime}
          */
         this.runtime = runtime;
+
+        this.activeThread = null;
     }
 
     /**
@@ -97,8 +99,9 @@ class Sequencer {
             numActiveThreads = 0;
             let stoppedThread = false;
             // Attempt to run each thread one time.
-            for (let i = 0; i < this.runtime.threads.length; i++) {
-                const activeThread = this.runtime.threads[i];
+            const threads = this.runtime.threads;
+            for (let i = 0; i < threads.length; i++) {
+                const activeThread = this.activeThread = threads[i];
                 // Check if the thread is done so it is not executed.
                 if (activeThread.stack.length === 0 ||
                     activeThread.status === Thread.STATUS_DONE) {
@@ -165,6 +168,8 @@ class Sequencer {
             }
         }
 
+        this.activeThread = null;
+
         return doneThreads;
     }
 
diff --git a/test/fixtures/execute/control-stop-all-leaks.sb2 b/test/fixtures/execute/control-stop-all-leaks.sb2
new file mode 100644
index 000000000..fb0ea115a
Binary files /dev/null and b/test/fixtures/execute/control-stop-all-leaks.sb2 differ