diff --git a/CHANGES.md b/CHANGES.md
index 4e9445007c4..72e9a4bc9ad 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -14,6 +14,9 @@
 - Fix `dune --version`. The bootstrap didn't compute the version
   correctly. (#2929, fixes #2911, @diml)
 
+- Do not open the log file in `dune clean`. (#2965, fixes #2964 and
+  #2921, @diml)
+
 2.0.0 (20/11/2019)
 ------------------
 
diff --git a/bin/common.ml b/bin/common.ml
index db26d7de3fd..c996a0bf126 100644
--- a/bin/common.ml
+++ b/bin/common.ml
@@ -68,9 +68,9 @@ let set_dirs c =
   Path.set_root (Path.External.cwd ());
   Path.Build.set_build_dir (Path.Build.Kind.of_string c.build_dir)
 
-let set_common_other c ~targets =
+let set_common_other ?log_file c ~targets =
   Console.init c.config.display;
-  Log.init ();
+  Log.init () ?file:log_file;
   Clflags.debug_dep_path := c.debug_dep_path;
   Clflags.debug_findlib := c.debug_findlib;
   Clflags.debug_backtraces := c.debug_backtraces;
@@ -92,9 +92,9 @@ let set_common_other c ~targets =
   Clflags.ignore_promoted_rules := c.ignore_promoted_rules;
   Option.iter ~f:Dune.Stats.enable c.stats_trace_file
 
-let set_common c ~targets =
+let set_common ?log_file c ~targets =
   set_dirs c;
-  set_common_other c ~targets
+  set_common_other ?log_file c ~targets
 
 let footer =
   `Blocks
diff --git a/bin/common.mli b/bin/common.mli
index d0dd8ea02ad..1e83b4ebd12 100644
--- a/bin/common.mli
+++ b/bin/common.mli
@@ -1,3 +1,5 @@
+open Stdune
+
 type t
 
 val workspace_file : t -> Arg.Path.t option
@@ -20,16 +22,17 @@ val default_target : t -> Arg.Dep.t
 
 val prefix_target : t -> string -> string
 
-(** [set_common common ~targets] is [set_dirs common] followed by
+(** [set_common ?log common ~targets] is [set_dirs common] followed by
     [set_common_other common ~targets]. In general, [set_common] executes
     sequence of side-effecting actions to initialize Dune's working environment
-    based on the options determined in a [Common.t] record *)
-val set_common : t -> targets:Arg.Dep.t list -> unit
+    based on the options determined in a [Common.t] record.contents. *)
+val set_common : ?log_file:Log.File.t -> t -> targets:Arg.Dep.t list -> unit
 
 (** [set_common_other common ~targets] sets all stateful values dictated by
     [common], except those accounted for by [set_dirs]. [targets] are used to
     obtain external library dependency hints, if needed. *)
-val set_common_other : t -> targets:Arg.Dep.t list -> unit
+val set_common_other :
+  ?log_file:Log.File.t -> t -> targets:Arg.Dep.t list -> unit
 
 (** [set_dirs common] sets the workspace root and build directories, and makes
     the root the current working directory *)
diff --git a/bin/main.ml b/bin/main.ml
index b3021fc138c..8d50ece8f79 100644
--- a/bin/main.ml
+++ b/bin/main.ml
@@ -89,7 +89,12 @@ let clean =
   in
   let term =
     let+ common = Common.term in
-    Common.set_common common ~targets:[];
+    (* Pass [No_log_file] to prevent the log file from being created. Indeed, we
+       are going to delete the whole build directory right after and that
+       includes deleting the log file. Not only creating the log file would be
+       useless but with some FS this also causes [dune clean] to fail (cf
+       https://github.com/ocaml/dune/issues/2964). *)
+    Common.set_common common ~targets:[] ~log_file:No_log_file;
     Build_system.files_in_source_tree_to_delete ()
     |> Path.Set.iter ~f:Path.unlink_no_err;
     Path.rm_rf Path.build_dir