diff --git a/doc/changes/10671.md b/doc/changes/10671.md
new file mode 100644
index 00000000000..3887e4031bd
--- /dev/null
+++ b/doc/changes/10671.md
@@ -0,0 +1 @@
+- Expect test fixes: support multiple modes and fix dependencies when there is a custom runner (#10671, @vouillon)
diff --git a/src/dune_rules/test_rules.ml b/src/dune_rules/test_rules.ml
index e27d34c934d..53ea8b62a51 100644
--- a/src/dune_rules/test_rules.ml
+++ b/src/dune_rules/test_rules.ml
@@ -1,14 +1,14 @@
 open Import
 
 let rules (t : Tests.t) ~sctx ~dir ~scope ~expander ~dir_contents =
-  let test_kind (loc, name) =
+  let test_kind (loc, name, ext) =
     let files = Dir_contents.text_files dir_contents in
     let expected_basename = name ^ ".expected" in
     if Filename.Set.mem files expected_basename
     then
       `Expect
         { Diff.file1 = String_with_vars.make_text loc expected_basename
-        ; file2 = String_with_vars.make_text loc (name ^ ".output")
+        ; file2 = String_with_vars.make_text loc (name ^ ext ^ ".output")
         ; optional = false
         ; mode = Text
         }
@@ -70,19 +70,20 @@ let rules (t : Tests.t) ~sctx ~dir ~scope ~expander ~dir_contents =
           | `js -> Jsoo_rules.js_of_ocaml_runtest_alias ~dir
           | `exe | `bc -> Memo.return Alias0.runtest
         in
+        let deps =
+          match custom_runner with
+          | Some _ ->
+            Bindings.Unnamed (Dep_conf.File (String_with_vars.make_text loc test_exe))
+            :: t.deps
+          | None -> t.deps
+        in
         let add_alias ~loc ~action ~locks =
           (* CR-rgrinberg: why are we going through the stanza api? *)
           let alias =
             { Alias_conf.name = runtest_alias
             ; locks
             ; package = t.package
-            ; deps =
-                (match custom_runner with
-                 | Some _ ->
-                   Bindings.Unnamed
-                     (Dep_conf.File (String_with_vars.make_text loc test_exe))
-                   :: t.deps
-                 | None -> t.deps)
+            ; deps
             ; action = Some (loc, action)
             ; enabled_if = t.enabled_if
             ; loc
@@ -90,12 +91,12 @@ let rules (t : Tests.t) ~sctx ~dir ~scope ~expander ~dir_contents =
           in
           Simple_rules.alias sctx ~extra_bindings ~dir ~expander alias
         in
-        match test_kind (loc, s) with
+        match test_kind (loc, s, ext) with
         | `Regular -> add_alias ~loc ~action:run_action ~locks:[]
         | `Expect diff ->
           let rule =
             { Rule_conf.targets = Infer
-            ; deps = t.deps
+            ; deps
             ; action =
                 ( loc
                 , Action_unexpanded.Redirect_out (Stdout, diff.file2, Normal, run_action)
diff --git a/test/blackbox-tests/test-cases/jsoo/tests.t/b.expected b/test/blackbox-tests/test-cases/jsoo/tests.t/b.expected
new file mode 100644
index 00000000000..3aca7c21f74
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/tests.t/b.expected
@@ -0,0 +1 @@
+b: ok
diff --git a/test/blackbox-tests/test-cases/jsoo/tests.t/run.t b/test/blackbox-tests/test-cases/jsoo/tests.t/run.t
index 31412302c01..1debd3da900 100644
--- a/test/blackbox-tests/test-cases/jsoo/tests.t/run.t
+++ b/test/blackbox-tests/test-cases/jsoo/tests.t/run.t
@@ -2,4 +2,3 @@ tests stanza with jsoo
 
   $ dune build @default @runtest-js
   a: ok
-  b: ok
diff --git a/test/blackbox-tests/test-cases/tests-stanza-expected-deps.t b/test/blackbox-tests/test-cases/tests-stanza-expected-deps.t
index 1fe61a4f8eb..5d8897a7f8b 100644
--- a/test/blackbox-tests/test-cases/tests-stanza-expected-deps.t
+++ b/test/blackbox-tests/test-cases/tests-stanza-expected-deps.t
@@ -23,4 +23,4 @@ This is visible when trying to build the `@all` alias. See #5950.
 
   $ cp data.txt t.expected
 
-  $ dune build t.output
+  $ dune build t.exe.output
diff --git a/test/blackbox-tests/test-cases/tests-stanza/generated.t/run.t b/test/blackbox-tests/test-cases/tests-stanza/generated.t/run.t
index f041a30b27a..58dbb66f070 100644
--- a/test/blackbox-tests/test-cases/tests-stanza/generated.t/run.t
+++ b/test/blackbox-tests/test-cases/tests-stanza/generated.t/run.t
@@ -1,5 +1,5 @@
   $ dune runtest
   File "generated.expected", line 1, characters 0-0:
   Error: Files _build/default/generated.expected and
-  _build/default/generated.output differ.
+  _build/default/generated.exe.output differ.
   [1]
diff --git a/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune b/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune
new file mode 100644
index 00000000000..9137703f0ac
--- /dev/null
+++ b/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune
@@ -0,0 +1 @@
+(test (name modes) (modes byte native))
diff --git a/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune-project b/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune-project
new file mode 100644
index 00000000000..37f995d6492
--- /dev/null
+++ b/test/blackbox-tests/test-cases/tests-stanza/modes.t/dune-project
@@ -0,0 +1 @@
+(lang dune 3.0)
diff --git a/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.expected b/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.expected
new file mode 100644
index 00000000000..afba1fb71ea
--- /dev/null
+++ b/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.expected
@@ -0,0 +1 @@
+testing multiple modes
diff --git a/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.ml b/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.ml
new file mode 100644
index 00000000000..9c7d02e4c69
--- /dev/null
+++ b/test/blackbox-tests/test-cases/tests-stanza/modes.t/modes.ml
@@ -0,0 +1 @@
+print_endline "testing multiple modes"
diff --git a/test/blackbox-tests/test-cases/tests-stanza/modes.t/run.t b/test/blackbox-tests/test-cases/tests-stanza/modes.t/run.t
new file mode 100644
index 00000000000..10bcbf13621
--- /dev/null
+++ b/test/blackbox-tests/test-cases/tests-stanza/modes.t/run.t
@@ -0,0 +1 @@
+  $ dune runtest