diff --git a/test/blackbox-tests/dune.inc b/test/blackbox-tests/dune.inc
index 80a06411592..4b627ca6b07 100644
--- a/test/blackbox-tests/dune.inc
+++ b/test/blackbox-tests/dune.inc
@@ -755,6 +755,14 @@
    test-cases/github24
    (progn (run %{exe:cram.exe} -test run.t) (diff? run.t run.t.corrected)))))
 
+(alias
+ (name github2499)
+ (deps (package dune) (source_tree test-cases/github2499))
+ (action
+  (chdir
+   test-cases/github2499
+   (progn (run %{exe:cram.exe} -test run.t) (diff? run.t run.t.corrected)))))
+
 (alias
  (name github25)
  (deps (package dune) (source_tree test-cases/github25))
@@ -1789,6 +1797,7 @@
   (alias github2228)
   (alias github2272)
   (alias github24)
+  (alias github2499)
   (alias github25)
   (alias github534)
   (alias github568)
@@ -1987,6 +1996,7 @@
   (alias github2228)
   (alias github2272)
   (alias github24)
+  (alias github2499)
   (alias github25)
   (alias github534)
   (alias github568)
diff --git a/test/blackbox-tests/test-cases/github2499/run.t b/test/blackbox-tests/test-cases/github2499/run.t
new file mode 100644
index 00000000000..105c4165e86
--- /dev/null
+++ b/test/blackbox-tests/test-cases/github2499/run.t
@@ -0,0 +1,28 @@
+Reproduction case for #2499: dune doesn't cleanup stale directories
+
+  $ cat >dune-project <<EOF
+  > (lang dune 2.0)
+  > EOF
+
+  $ cat >dune <<EOF
+  > (data_only_dirs data)
+  > (rule
+  >  (deps (source_tree data))
+  >  (action (with-stdout-to list (system "find data -type f | sort"))))
+  > EOF
+
+
+  $ mkdir -p data/{a,b}
+  $ touch data/{a,b}/x
+
+  $ dune build list
+  $ cat _build/default/list
+  data/a/x
+  data/b/x
+
+  $ rm -rf data/b
+
+  $ dune build list
+  $ cat _build/default/list
+  data/a/x
+  data/b/x