diff --git a/bin/common.ml b/bin/common.ml
index 1fe5c04ad012..4bf398e946cb 100644
--- a/bin/common.ml
+++ b/bin/common.ml
@@ -99,7 +99,9 @@ let set_common_other ?log_file c ~targets =
   Clflags.ignore_promoted_rules := c.ignore_promoted_rules;
   Option.iter ~f:Dune.Stats.enable c.stats_trace_file
 
-let set_common ?log_file c ~targets =
+let set_common ?log_file ?external_lib_deps_mode c ~targets =
+  Option.iter external_lib_deps_mode ~f:(fun x ->
+      Clflags.external_lib_deps_mode := x);
   set_dirs c;
   set_common_other ?log_file c ~targets
 
diff --git a/bin/common.mli b/bin/common.mli
index f143d6978650..7dc947802e3c 100644
--- a/bin/common.mli
+++ b/bin/common.mli
@@ -28,12 +28,17 @@ val default_target : t -> Arg.Dep.t
 
 val prefix_target : t -> string -> string
 
-(** [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.contents. *)
+(** [set_common ?log common ~targets ~external_lib_deps_mode] 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.contents. *)
 val set_common :
-  ?log_file:Dune_util.Log.File.t -> t -> targets:Arg.Dep.t list -> unit
+     ?log_file:Dune_util.Log.File.t
+  -> ?external_lib_deps_mode:bool
+  -> 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
diff --git a/bin/compute.ml b/bin/compute.ml
index ba38c15990e5..b0f8e64c5cac 100644
--- a/bin/compute.ml
+++ b/bin/compute.ml
@@ -29,13 +29,11 @@ let term =
          & info [] ~docv:"INPUT"
              ~doc:"Use $(docv) as the input to the function.")
      in
-     Common.set_common common ~targets:[];
+     Common.set_common common ~targets:[] ~external_lib_deps_mode:true;
      let action =
        Scheduler.go ~common (fun () ->
            let open Fiber.O in
-           let* _setup =
-             Import.Main.setup common ~external_lib_deps_mode:true
-           in
+           let* _setup = Import.Main.setup common in
            match (fn, inp) with
            | "list", None -> Fiber.return `List
            | "list", Some _ ->
diff --git a/bin/describe.ml b/bin/describe.ml
index 0ff22fa4fa0a..3d21bbab8abd 100644
--- a/bin/describe.ml
+++ b/bin/describe.ml
@@ -188,11 +188,11 @@ let term =
   and+ context_name = Common.context_arg ~doc:"Build context to use."
   and+ format = Format.arg
   and+ lang = Lang.arg in
-  Common.set_common common ~targets:[];
+  Common.set_common common ~targets:[] ~external_lib_deps_mode:false;
   let what = What.parse what ~lang in
   Scheduler.go ~common (fun () ->
       let open Fiber.O in
-      let* setup = Import.Main.setup common ~external_lib_deps_mode:false in
+      let* setup = Import.Main.setup common in
       let context =
         Import.Main.find_context_exn setup.workspace ~name:context_name
       in
diff --git a/bin/external_lib_deps.ml b/bin/external_lib_deps.ml
index 2a6ee7421d4f..8673faca7510 100644
--- a/bin/external_lib_deps.ml
+++ b/bin/external_lib_deps.ml
@@ -130,11 +130,11 @@ let term =
   and+ sexp =
     Arg.(value & flag & info [ "sexp" ] ~doc:{|Produce a s-expression output|})
   in
-  Common.set_common common ~targets:[];
+  Common.set_common common ~targets:[] ~external_lib_deps_mode:true;
   let setup, lib_deps =
     Scheduler.go ~common (fun () ->
         let open Fiber.O in
-        let+ setup = Import.Main.setup common ~external_lib_deps_mode:true in
+        let+ setup = Import.Main.setup common in
         let targets = Target.resolve_targets_exn common setup targets in
         let request = Target.request targets in
         let deps = Build_system.all_lib_deps ~request in
diff --git a/bin/import.ml b/bin/import.ml
index 477b66bc4d15..676f87d84048 100644
--- a/bin/import.ml
+++ b/bin/import.ml
@@ -79,7 +79,7 @@ module Main = struct
     let ancestor_vcs = (Common.root common).ancestor_vcs in
     scan_workspace ?workspace_file ?x ?profile ~capture_outputs ~ancestor_vcs ()
 
-  let setup ?external_lib_deps_mode common =
+  let setup common =
     let open Fiber.O in
     let* caching = make_cache (Common.config common) in
     let* workspace = scan_workspace common in
@@ -121,7 +121,7 @@ module Main = struct
     in
     init_build_system workspace
       ~sandboxing_preference:(Common.config common).sandboxing_preference
-      ?caching ?external_lib_deps_mode ?only_packages
+      ?caching ?only_packages
 end
 
 module Scheduler = struct
diff --git a/bin/print_rules.ml b/bin/print_rules.ml
index 2e322bfbd694..52d42edc90f3 100644
--- a/bin/print_rules.ml
+++ b/bin/print_rules.ml
@@ -109,10 +109,10 @@ let term =
   and+ targets = Arg.(value & pos_all string [] & Arg.info [] ~docv:"TARGET") in
   let out = Option.map ~f:Path.of_string out in
   let targets = List.map ~f:Arg.Dep.file targets in
-  Common.set_common common ~targets;
+  Common.set_common common ~targets ~external_lib_deps_mode:true;
   Scheduler.go ~common (fun () ->
       let open Fiber.O in
-      let* setup = Import.Main.setup common ~external_lib_deps_mode:true in
+      let* setup = Import.Main.setup common in
       let request =
         match targets with
         | [] ->
diff --git a/src/dune/clflags.ml b/src/dune/clflags.ml
index 342e167f72ed..243478563cc9 100644
--- a/src/dune/clflags.ml
+++ b/src/dune/clflags.ml
@@ -10,6 +10,8 @@ let debug_dep_path = ref false
 
 let external_lib_deps_hint = ref []
 
+let external_lib_deps_mode = ref false
+
 let capture_outputs = ref true
 
 let debug_backtraces = Dune_util.Report_error.report_backtraces
diff --git a/src/dune/clflags.mli b/src/dune/clflags.mli
index 91bcb0a93f3d..84ff6d07a181 100644
--- a/src/dune/clflags.mli
+++ b/src/dune/clflags.mli
@@ -9,6 +9,8 @@ val debug_findlib : bool ref
 (** The command line for "Hint: try: dune external-lib-deps ..." *)
 val external_lib_deps_hint : string list ref
 
+val external_lib_deps_mode : bool ref
+
 (** Capture the output of sub-commands *)
 val capture_outputs : bool ref
 
diff --git a/src/dune/gen_rules.ml b/src/dune/gen_rules.ml
index 898fb7717ab3..7dcbba6777f3 100644
--- a/src/dune/gen_rules.ml
+++ b/src/dune/gen_rules.ml
@@ -402,7 +402,7 @@ let filter_out_stanzas_from_hidden_packages ~visible_pkgs =
                  { implementation = name; virtual_lib; variant; project; loc })
           | _ -> None ))
 
-let gen ~contexts ?(external_lib_deps_mode = false) ?only_packages conf =
+let gen ~contexts ?only_packages conf =
   let open Fiber.O in
   let { Dune_load.dune_files; packages; projects } = conf in
   let packages = Option.value only_packages ~default:packages in
@@ -432,8 +432,7 @@ let gen ~contexts ?(external_lib_deps_mode = false) ?only_packages conf =
     in
     let* host, stanzas = Fiber.fork_and_join host stanzas in
     let sctx =
-      Super_context.create ?host ~context ~projects ~packages
-        ~external_lib_deps_mode ~stanzas
+      Super_context.create ?host ~context ~projects ~packages ~stanzas
     in
     let+ () = Fiber.Ivar.fill (Table.find_exn sctxs context.name) sctx in
     (context.name, sctx)
diff --git a/src/dune/gen_rules.mli b/src/dune/gen_rules.mli
index af026b9ee23f..ea05dcdb38d4 100644
--- a/src/dune/gen_rules.mli
+++ b/src/dune/gen_rules.mli
@@ -4,7 +4,6 @@ open! Import
 (* Generate rules. Returns evaluated Dune files per context names. *)
 val gen :
      contexts:Context.t list
-  -> ?external_lib_deps_mode:bool (* default: false *)
   -> ?only_packages:Package.t Package.Name.Map.t
   -> Dune_load.conf
   -> Super_context.t Context_name.Map.t Fiber.t
diff --git a/src/dune/install_rules.ml b/src/dune/install_rules.ml
index 5d5d59def488..99d3882e0e83 100644
--- a/src/dune/install_rules.ml
+++ b/src/dune/install_rules.ml
@@ -174,7 +174,7 @@ end = struct
   let stanzas_to_entries sctx =
     let ctx = Super_context.context sctx in
     let stanzas = Super_context.stanzas sctx in
-    let external_lib_deps_mode = Super_context.external_lib_deps_mode sctx in
+    let external_lib_deps_mode = !Clflags.external_lib_deps_mode in
     let keep_if = keep_if ~external_lib_deps_mode in
     let init =
       Super_context.packages sctx
diff --git a/src/dune/lib.ml b/src/dune/lib.ml
index 4852d71f3e52..0e04ac3a5436 100644
--- a/src/dune/lib.ml
+++ b/src/dune/lib.ml
@@ -1918,7 +1918,7 @@ module DB = struct
         | Some (Found lib) -> Found lib)
       ~all:(fun () -> Lib_name.Map.keys map)
 
-  let create_from_findlib ~external_lib_deps_mode ~stdlib_dir findlib =
+  let create_from_findlib ~stdlib_dir findlib =
     create () ~parent:None ~stdlib_dir
       ~resolve:(fun name ->
         match Findlib.find findlib name with
@@ -1930,7 +1930,7 @@ module DB = struct
           match e with
           | Invalid_dune_package why -> Invalid why
           | Not_found ->
-            if external_lib_deps_mode then
+            if !Clflags.external_lib_deps_mode then
               let pkg = Findlib.dummy_lib findlib ~name in
               Found (Dune_package.Lib.info pkg)
             else
diff --git a/src/dune/lib.mli b/src/dune/lib.mli
index 7d71e1b8f032..af79098ffff9 100644
--- a/src/dune/lib.mli
+++ b/src/dune/lib.mli
@@ -194,8 +194,7 @@ module DB : sig
     -> Library_related_stanza.t list
     -> t
 
-  val create_from_findlib :
-    external_lib_deps_mode:bool -> stdlib_dir:Path.t -> Findlib.t -> t
+  val create_from_findlib : stdlib_dir:Path.t -> Findlib.t -> t
 
   val find : t -> Lib_name.t -> lib option
 
diff --git a/src/dune/main.ml b/src/dune/main.ml
index afe8e60b2624..f7ca96e4d401 100644
--- a/src/dune/main.ml
+++ b/src/dune/main.ml
@@ -68,14 +68,10 @@ let scan_workspace ?workspace_file ?x ?(capture_outputs = true) ?profile
         ]);
   { contexts; conf; env }
 
-let init_build_system ?only_packages ?external_lib_deps_mode
-    ~sandboxing_preference ?caching w =
+let init_build_system ?only_packages ~sandboxing_preference ?caching w =
   Build_system.reset ();
   Build_system.init ~sandboxing_preference ~contexts:w.contexts ?caching;
-  let+ scontexts =
-    Gen_rules.gen w.conf ~contexts:w.contexts ?only_packages
-      ?external_lib_deps_mode
-  in
+  let+ scontexts = Gen_rules.gen w.conf ~contexts:w.contexts ?only_packages in
   { workspace = w; scontexts }
 
 let auto_concurrency =
diff --git a/src/dune/main.mli b/src/dune/main.mli
index f558e6a41bf2..8cf3422f4b77 100644
--- a/src/dune/main.mli
+++ b/src/dune/main.mli
@@ -29,7 +29,6 @@ val scan_workspace :
 (** Load dune files and initializes the build system *)
 val init_build_system :
      ?only_packages:Package.t Package.Name.Map.t
-  -> ?external_lib_deps_mode:bool
   -> sandboxing_preference:Sandbox_mode.t list
   -> ?caching:Build_system.caching
   -> workspace
diff --git a/src/dune/super_context.ml b/src/dune/super_context.ml
index 1733790bac1a..040addd27a7b 100644
--- a/src/dune/super_context.ml
+++ b/src/dune/super_context.ml
@@ -186,7 +186,6 @@ type t =
   ; lib_entries_by_package : Lib_entry.t list Package.Name.Map.t
   ; env_tree : Env_tree.t
   ; dir_status_db : Dir_status.DB.t
-  ; external_lib_deps_mode : bool
   ; (* Env node that represents the environment configured for the workspace. It
        is used as default at the root of every project in the workspace. *)
     default_env : Env_node.t Memo.Lazy.t
@@ -207,8 +206,6 @@ let build_dir t = t.context.build_dir
 
 let profile t = t.context.profile
 
-let external_lib_deps_mode t = t.external_lib_deps_mode
-
 let equal = (( == ) : t -> t -> bool)
 
 let hash t = Context.hash t.context
@@ -415,13 +412,11 @@ let get_installed_binaries stanzas ~(context : Context.t) =
           acc
       | _ -> acc)
 
-let create ~(context : Context.t) ?host ~projects ~packages ~stanzas
-    ~external_lib_deps_mode =
+let create ~(context : Context.t) ?host ~projects ~packages ~stanzas =
   let lib_config = Context.lib_config context in
   let installed_libs =
     let stdlib_dir = context.stdlib_dir in
     Lib.DB.create_from_findlib context.findlib ~stdlib_dir
-      ~external_lib_deps_mode
   in
   let scopes, public_libs =
     Scope.DB.create_from_stanzas ~projects ~context ~installed_libs ~lib_config
@@ -528,7 +523,6 @@ let create ~(context : Context.t) ?host ~projects ~packages ~stanzas
                   Lib_name.compare (Lib_entry.name a) (Lib_entry.name b)))
   ; env_tree
   ; default_env
-  ; external_lib_deps_mode
   ; dir_status_db
   ; projects_by_key
   }
diff --git a/src/dune/super_context.mli b/src/dune/super_context.mli
index bc02452c0779..22ed28de8bf6 100644
--- a/src/dune/super_context.mli
+++ b/src/dune/super_context.mli
@@ -16,7 +16,6 @@ val create :
   -> projects:Dune_project.t list
   -> packages:Package.t Package.Name.Map.t
   -> stanzas:Dune_load.Dune_file.t list
-  -> external_lib_deps_mode:bool
   -> t
 
 val context : t -> Context.t
@@ -36,8 +35,6 @@ val profile : t -> Profile.t
 
 val host : t -> t
 
-val external_lib_deps_mode : t -> bool
-
 module Lib_entry : sig
   type t =
     | Library of Lib.Local.t