diff --git a/src/laminar.cpp b/src/laminar.cpp
index fb5e229..2a42f24 100644
--- a/src/laminar.cpp
+++ b/src/laminar.cpp
@@ -587,7 +587,7 @@ void Laminar::notifyConfigChanged()
 
 void Laminar::abortAll() {
     for(std::shared_ptr<Run> run : activeJobs) {
-        run->abort();
+        run->abort(false);
     }
 }
 
@@ -674,13 +674,13 @@ bool Laminar::tryStartRun(std::shared_ptr<Run> run, int queueIndex) {
             run->addScript((cfgDir/"jobs"/run->name+".run").string());
             // job after-run script
             if(fs::exists(cfgDir/"jobs"/run->name+".after"))
-                run->addScript((cfgDir/"jobs"/run->name+".after").string());
+                run->addScript((cfgDir/"jobs"/run->name+".after").string(), true);
             // per-node after-run script
             if(fs::exists(cfgDir/"nodes"/node->name+".after"))
-                run->addScript((cfgDir/"nodes"/node->name+".after").string());
+                run->addScript((cfgDir/"nodes"/node->name+".after").string(), true);
             // global after-run script
             if(fs::exists(cfgDir/"after"))
-                run->addScript((cfgDir/"after").string());
+                run->addScript((cfgDir/"after").string(), true);
 
             // add environment files
             if(fs::exists(cfgDir/"env"))
@@ -699,7 +699,7 @@ bool Laminar::tryStartRun(std::shared_ptr<Run> run, int queueIndex) {
                     // will be cancelled and the callback never called.
                     Run* r = run.get();
                     r->timeout = srv->addTimeout(timeout, [r](){
-                        r->abort();
+                        r->abort(true);
                     });
                 }
             }
diff --git a/src/run.cpp b/src/run.cpp
index 3b3186f..9f84a2f 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -128,17 +128,17 @@ bool Run::step() {
     return false;
 }
 
-void Run::addScript(std::string scriptPath, std::string scriptWorkingDir) {
-    scripts.push({scriptPath, scriptWorkingDir});
+void Run::addScript(std::string scriptPath, std::string scriptWorkingDir, bool runOnAbort) {
+    scripts.push({scriptPath, scriptWorkingDir, runOnAbort});
 }
 
 void Run::addEnv(std::string path) {
     env.push_back(path);
 }
 
-void Run::abort() {
-    // clear all pending scripts
-    std::queue<Script>().swap(scripts);
+void Run::abort(bool respectRunOnAbort) {
+    while(scripts.size() && (!respectRunOnAbort || !scripts.front().runOnAbort))
+        scripts.pop();
     // if the Maybe is empty, wait() was already called on this process
     KJ_IF_MAYBE(p, current_pid) {
         kill(-*p, SIGTERM);
diff --git a/src/run.h b/src/run.h
index fe3021a..9d38074 100644
--- a/src/run.h
+++ b/src/run.h
@@ -56,16 +56,16 @@ public:
     bool step();
 
     // adds a script to the queue of scripts to be executed by this run
-    void addScript(std::string scriptPath, std::string scriptWorkingDir);
+    void addScript(std::string scriptPath, std::string scriptWorkingDir, bool runOnAbort = false);
 
     // adds a script to the queue using the runDir as the scripts CWD
-    void addScript(std::string script) { addScript(script, runDir); }
+    void addScript(std::string script, bool runOnAbort = false) { addScript(script, runDir, runOnAbort); }
 
     // adds an environment file that will be sourced before this run
     void addEnv(std::string path);
 
     // aborts this run
-    void abort();
+    void abort(bool respectRunOnAbort);
 
     // called when a process owned by this run has been reaped. The status
     // may be used to set the run's job status
@@ -96,6 +96,7 @@ private:
     struct Script {
         std::string path;
         std::string cwd;
+        bool runOnAbort;
     };
 
     std::queue<Script> scripts;
diff --git a/test/test-run.cpp b/test/test-run.cpp
index 32b5cc2..833389f 100644
--- a/test/test-run.cpp
+++ b/test/test-run.cpp
@@ -105,7 +105,7 @@ TEST_F(RunTest, Abort) {
     run.addScript("/usr/bin/yes");
     run.step();
     usleep(200); // TODO fix
-    run.abort();
+    run.abort(false);
     wait();
     EXPECT_EQ(RunState::ABORTED, run.result);
 }
@@ -116,7 +116,7 @@ TEST_F(RunTest, AbortAfterFailed) {
     run.addScript("/usr/bin/yes");
     run.step();
     usleep(200); // TODO fix
-    run.abort();
+    run.abort(false);
     wait();
     EXPECT_EQ(RunState::FAILED, run.result);
 }