diff --git a/amlb/utils/process.py b/amlb/utils/process.py
index 97c557a86..3752f85b3 100644
--- a/amlb/utils/process.py
+++ b/amlb/utils/process.py
@@ -49,6 +49,10 @@ def file_lock(path, timeout=-1):
         yield
 
 
+class StaleProcessError(subprocess.TimeoutExpired):
+    pass
+
+
 def run_subprocess(
     *popenargs,
     input=None,
@@ -104,7 +108,16 @@ def communicate(process, input=None, timeout=None):
         except:  # also handles kb interrupts
             process.kill()
             raise
+
         retcode = process.poll()
+        if retcode is None:
+            # Process still lives => communication stopped because of activity timeout
+            process.kill()
+            process.wait()
+            raise StaleProcessError(
+                process.args, float("nan"), output=stdout, stderr=stderr
+            )
+
         if check and retcode:
             raise subprocess.CalledProcessError(
                 retcode, process.args, output=stdout, stderr=stderr
@@ -186,6 +199,9 @@ def read_pipe(pipe, timeout):
         pipes = as_list(pipe)
         # wait until a pipe is ready for reading, non-Windows only.
         ready, *_ = select.select(pipes, [], [], timeout)
+        # if a pipe is not ready it could be timeout or it could be end of process
+        # so at this point we do not know. Only after the communicate function is over do we know.
+        # i.e., if the process is still running it does not have a retcode.
         reads = [""] * len(pipes)
         # print update for each pipe that is ready for reading
         for i, p in enumerate(pipes):
@@ -315,8 +331,6 @@ def communicate(*args, **kwargs):
             log.log(params.output_level, e.stdout)
         if e.stderr:
             log.log(params.error_level, e.stderr)
-        # error_tail = tail(e.stderr, 25) if e.stderr else 'Unknown Error'
-        # raise subprocess.SubprocessError("Error when running command `{cmd}`: {error}".format(cmd=full_cmd, error=error_tail))
         raise e
 
 
diff --git a/resources/config.yaml b/resources/config.yaml
index d9976b1f6..b990f43d1 100644
--- a/resources/config.yaml
+++ b/resources/config.yaml
@@ -27,6 +27,7 @@ archive: ['logs']       # list of output folders that should be archived by defa
 setup:                   # configuration namespace for the framework setup phase.
   live_output: true      # set to true to stream the output of setup commands, if false they are only printed when setup is complete.
   activity_timeout: 600  # when using live output, subprocess will be considered as hanging if nothing was printed during this activity time.
+                         # No effect is live_output is set to 'False'.
 
 frameworks:              # configuration namespace for the frameworks definitions.
   definition_file:       # list of yaml files describing the frameworks base definitions.
diff --git a/runbenchmark.py b/runbenchmark.py
index 00cfef132..431e865ef 100644
--- a/runbenchmark.py
+++ b/runbenchmark.py
@@ -18,6 +18,8 @@
     str2bool,
     str_sanitize,
     zip_path,
+    StaleProcessError,
+    Namespace,
 )
 from amlb import log, AutoMLError
 from amlb.defaults import default_dirs
@@ -358,9 +360,19 @@
             args.mode,
         )
 
-    bench.setup(amlb.SetupMode[args.setup])
-    if args.setup != "only":
-        res = bench.run(args.task, args.fold)
+    try:
+        bench.setup(amlb.SetupMode[args.setup])
+    except StaleProcessError as e:
+        setting = "setup.activity_timeout"
+        timeout = Namespace.get(amlb_res.config, setting)
+        log.error(
+            f"Process '{e.cmd}' was aborted after producing no output for {timeout} seconds. "
+            f"If the process is expected to take more time, please raise the '{setting}' limit."
+        )
+        exit_code = 1
+    else:
+        if args.setup != "only":
+            res = bench.run(args.task, args.fold)
 except (ValueError, AutoMLError) as e:
     log.error("\nERROR:\n%s", e)
     if extras.get("verbose") is True:
diff --git a/tests/unit/amlb/utils/process/test_run.py b/tests/unit/amlb/utils/process/test_run.py
new file mode 100644
index 000000000..e6df0d62d
--- /dev/null
+++ b/tests/unit/amlb/utils/process/test_run.py
@@ -0,0 +1,20 @@
+import pytest
+
+from amlb.utils import StaleProcessError, run_cmd
+
+
+@pytest.mark.parametrize("mode", ["line", "block", True])
+def test_subprocess_detects_stale_process(mode):
+    one_ms = 0.001
+    with pytest.raises(StaleProcessError):
+        run_cmd(f"sleep {one_ms}", _activity_timeout_=one_ms / 2, _live_output_=mode)
+
+
+def test_subprocess_does_not_raises_if_process_exits_early():
+    run_cmd("echo hi", _activity_timeout_=1, _live_output_=True)
+
+
+@pytest.mark.xfail(reason="Detection of stale processes currently requires output")
+def test_subprocess_does_not_raises_on_silent_process():
+    one_ms = 0.001
+    run_cmd(f"sleep {one_ms}", _activity_timeout_=one_ms / 2, _live_output_=True)