diff --git a/snakemake/dag.py b/snakemake/dag.py
index 655148e13..dad8cdec5 100755
--- a/snakemake/dag.py
+++ b/snakemake/dag.py
@@ -235,14 +235,15 @@ def update_jobids(self):
                 self._jobid[job] = len(self._jobid)
 
     def cleanup_workdir(self):
-        for io_dir in set(
-            os.path.dirname(io_file)
-            for job in self.jobs
-            for io_file in chain(job.output, job.input)
-            if not os.path.exists(io_file)
-        ):
-            if os.path.exists(io_dir) and not len(os.listdir(io_dir)):
-                os.removedirs(io_dir)
+        for job in self.jobs:
+            if not self.is_edit_notebook_job(job):
+                for io_dir, job in set(
+                    os.path.dirname(io_file)
+                    for io_file in chain(job.output, job.input)
+                    if not os.path.exists(io_file)
+                ):
+                    if os.path.exists(io_dir) and not len(os.listdir(io_dir)):
+                        os.removedirs(io_dir)
 
     def cleanup(self):
         self.job_cache.clear()
diff --git a/tests/test_jupyter_notebook_draft/Snakefile b/tests/test_jupyter_notebook_draft/Snakefile
index 0b7526f01..7d04d595c 100644
--- a/tests/test_jupyter_notebook_draft/Snakefile
+++ b/tests/test_jupyter_notebook_draft/Snakefile
@@ -16,7 +16,7 @@ rule bar:
     input:
         infile = 'data.txt'
     output:
-        outfile = 'result_intermediate.txt'
+        outfile = 'results/result_intermediate.txt'
     conda:
         'env.yaml'
     notebook:
@@ -24,7 +24,7 @@ rule bar:
 
 rule baz:
     input:
-        infile = 'result_intermediate.txt'
+        infile = 'results/result_intermediate.txt'
     output:
         outfile = 'result_final.txt'
     log:
@@ -37,7 +37,7 @@ rule baz:
 
 rule wild:
     input:
-        infile = 'result_intermediate.txt'
+        infile = 'results/result_intermediate.txt'
     output:
         outfile = '{what}.result_final.txt'
     conda:
diff --git a/tests/test_jupyter_notebook_draft/expected-results/results/.gitkeep b/tests/test_jupyter_notebook_draft/expected-results/results/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/tests.py b/tests/tests.py
index d9eacb628..b6e995c05 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1179,7 +1179,7 @@ def test_jupyter_notebook_draft():
         dpath("test_jupyter_notebook_draft"),
         use_conda=True,
         edit_notebook=EditMode(draft_only=True),
-        targets=["result_intermediate.txt"],
+        targets=["results/result_intermediate.txt"],
         check_md5=False,
     )