diff --git a/Changes.md b/Changes.md
index 2d62056459..b378538ec1 100644
--- a/Changes.md
+++ b/Changes.md
@@ -56,6 +56,9 @@ Unreleased
 - melange: allow installing melange in more OCaml versions and compiler
   switches. Melange now migrates binary AST to the version it understands
   ([#548](https://github.com/melange-re/melange/pull/548))
+- melange: don't run anonymous args function from
+  `[@@@bs.config {flags = [| ... |]}]` attributes
+  ([#554](https://github.com/melange-re/melange/pull/554))
 
 0.3.2 2022-11-19
 ---------------
diff --git a/flake.lock b/flake.lock
index c18c78c556..d948507357 100644
--- a/flake.lock
+++ b/flake.lock
@@ -64,11 +64,11 @@
         "nixpkgs": "nixpkgs_2"
       },
       "locked": {
-        "lastModified": 1682287386,
-        "narHash": "sha256-FKYZqW0GGRh5GFVpPlW/m7Xf0pCS/JKBflDTFCwDPpw=",
+        "lastModified": 1682455662,
+        "narHash": "sha256-8v3OUG5kjfDhuXBZFgdHAHqv741eZRro2WhKD7Odn/o=",
         "owner": "nix-ocaml",
         "repo": "nix-overlays",
-        "rev": "47c2c7838ebdcc434265744d4f198f5d03cecb03",
+        "rev": "d1bef8a898bdd5f348a67b6d766ea1fe9d1808fb",
         "type": "github"
       },
       "original": {
@@ -79,17 +79,17 @@
     },
     "nixpkgs_2": {
       "locked": {
-        "lastModified": 1682266827,
-        "narHash": "sha256-K+ZriFdFKMWbJ+IjJf3LJAKp3KePOvO76W2mzlxdsA4=",
+        "lastModified": 1682385804,
+        "narHash": "sha256-iK6k4jQ8jV3Lo79WkHQDugL/qTVqeynWXbdIcetZuMo=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "5d91a896449650d13fbba8c8abc65d1615c2b654",
+        "rev": "392218684aea34e48419ad57e690c6fd08aa3ea4",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "5d91a896449650d13fbba8c8abc65d1615c2b654",
+        "rev": "392218684aea34e48419ad57e690c6fd08aa3ea4",
         "type": "github"
       }
     },
diff --git a/jscomp/main/melc.ml b/jscomp/main/melc.ml
index aea0e0ecaa..d2a4ad20a1 100644
--- a/jscomp/main/melc.ml
+++ b/jscomp/main/melc.ml
@@ -73,34 +73,44 @@ let process_file sourcefile
 
 let ppf = Format.err_formatter
 
-let anonymous ~(rev_args : string list) =
-  if !Js_config.as_ppx then
-    match rev_args with
-    | [output; input] ->
-      `Ok (Melange_ppx_lib.Ppx_apply.apply_lazy
-        ~source:input
-        ~target:output
-        Melange_ppx_lib.Ppx_entry.rewrite_implementation
-        Melange_ppx_lib.Ppx_entry.rewrite_signature)
-    | _ -> `Error(false, "`--as-ppx` requires 2 arguments: `melc --as-ppx input output`")
-  else
-    begin
-        if !Js_config.syntax_only then begin
-          Ext_list.rev_iter rev_args (fun filename ->
-              begin
-                (* Clflags.reset_dump_state (); *)
-                (* Warnings.reset (); *)
-                process_file filename ppf
-              end );
-          `Ok ()
-          end else
+let anonymous =
+  let executed = ref false in
+  fun ~(rev_args : string list) ->
+    match !executed with
+    | true ->
+      (* Don't re-run anonymous arguments again if this function has already
+       * been executed. If this code is executing the 2nd time, it's coming
+       * from a [@bs.config { flags = [| ... |] }].. *)
+      `Ok ()
+    | false ->
+      executed := true;
+      if !Js_config.as_ppx then
+        match rev_args with
+        | [output; input] ->
+          `Ok (Melange_ppx_lib.Ppx_apply.apply_lazy
+            ~source:input
+            ~target:output
+            Melange_ppx_lib.Ppx_entry.rewrite_implementation
+            Melange_ppx_lib.Ppx_entry.rewrite_signature)
+        | _ -> `Error(false, "`--as-ppx` requires 2 arguments: `melc --as-ppx input output`")
+      else
+        begin
+            if !Js_config.syntax_only then begin
+              Ext_list.rev_iter rev_args (fun filename ->
+                  begin
+                    (* Clflags.reset_dump_state (); *)
+                    (* Warnings.reset (); *)
+                    process_file filename ppf
+                  end );
+              `Ok ()
+              end else
 
-      match rev_args with
-      | [filename] -> `Ok (process_file filename ppf)
-      | [] -> `Ok ()
-      | _ ->
-          `Error (false, "can not handle multiple files")
-    end
+          match rev_args with
+          | [filename] -> `Ok (process_file filename ppf)
+          | [] -> `Ok ()
+          | _ ->
+              `Error (false, "can not handle multiple files")
+        end
 
 (** used by -impl -intf *)
 let impl filename =
diff --git a/test/as-ppx-config-attribute.t b/test/as-ppx-config-attribute.t
new file mode 100644
index 0000000000..61710956ab
--- /dev/null
+++ b/test/as-ppx-config-attribute.t
@@ -0,0 +1,18 @@
+
+  $ cat > foo.ml <<EOF
+  > [@@@bs.config {flags = [| "-unsafe"; "-nopervasives" |] }]
+  > let x = 1
+  > EOF
+
+  $ melc foo.ml -as-pp foo.ml > foo.pp.ml
+  $ melc --as-ppx foo.pp.ml bar.pp.ml
+
+  $ melc ./bar.pp.ml
+  // Generated by Melange
+  'use strict';
+  
+  
+  var x = 1;
+  
+  exports.x = x;
+  /* No side effect */