diff --git a/src/app.js b/src/app.js
index 59ddc20b7e..eaf2e885e7 100644
--- a/src/app.js
+++ b/src/app.js
@@ -380,7 +380,6 @@ var run = function () {
     var fileNames = Object.keys(files.list())
 
     $filesEl.find('.file').remove()
-    $('#output').empty()
 
     for (var f in fileNames) {
       var name = fileNames[f]
@@ -815,6 +814,8 @@ var run = function () {
   })
 
   function runCompiler () {
+    if (transactionDebugger.isActive) return
+
     editorSyncFile()
     var currentFile = ui.get('currentFile')
     if (currentFile) {
diff --git a/src/app/debugger.js b/src/app/debugger.js
index 01fad6d1d1..035649a6a7 100644
--- a/src/app/debugger.js
+++ b/src/app/debugger.js
@@ -11,6 +11,7 @@ function Debugger (id, appAPI, executionContextEvent, editorEvent) {
   this.sourceMappingDecoder = new remix.util.SourceMappingDecoder()
   this.el.appendChild(this.debugger.render())
   this.appAPI = appAPI
+  this.isActive = false
 
   this.breakPointManager = new remix.code.BreakpointManager(this.debugger, (sourceLocation) => {
     return appAPI.offsetToLineColumn(sourceLocation, sourceLocation.file, this.editor, this.appAPI.lastCompilationResult().data)
@@ -33,8 +34,13 @@ function Debugger (id, appAPI, executionContextEvent, editorEvent) {
     self.switchProvider(context)
   })
 
+  this.debugger.event.register('newTraceLoaded', this, function () {
+    self.isActive = true
+  })
+
   this.debugger.event.register('traceUnloaded', this, function () {
     self.appAPI.currentSourceLocation(null)
+    self.isActive = false
   })
 
   // unload if a file has changed (but not if tabs were switched)