diff --git a/CHANGES.md b/CHANGES.md
index 1693a577f1c..1da6c875c8d 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -103,6 +103,9 @@ Unreleased
   useless and deprecated. Dune now conflicts with `merlin < 3.4.0` and
   `ocaml-lsp-server < 1.3.0` (#3554, @voodoos)
 
+- Remove non-existent `(native_archives ..)` entries in `dune-package` files in
+  bytecode only libraries. (#4041, @rgrinberg)
+
 2.7.1 (2/09/2020)
 -----------------
 
diff --git a/src/dune_rules/dune_file.ml b/src/dune_rules/dune_file.ml
index e2cd91d0a45..724033e7f14 100644
--- a/src/dune_rules/dune_file.ml
+++ b/src/dune_rules/dune_file.ml
@@ -838,7 +838,11 @@ module Library = struct
     let virtual_library = is_virtual conf in
     let foreign_archives = foreign_lib_files conf ~dir ~ext_lib in
     let native_archives =
-      [ Path.Build.relative dir (Lib_name.Local.to_string lib_name ^ ext_lib) ]
+      if modes.native then
+        [ Path.Build.relative dir (Lib_name.Local.to_string lib_name ^ ext_lib)
+        ]
+      else
+        []
     in
     let foreign_dll_files = foreign_dll_files conf ~dir ~ext_dll in
     let exit_module = Option.bind conf.stdlib ~f:(fun x -> x.exit_module) in
diff --git a/test/blackbox-tests/test-cases/dune-package.t/run.t b/test/blackbox-tests/test-cases/dune-package.t/run.t
index 8ad9311a5b5..2946e877c20 100644
--- a/test/blackbox-tests/test-cases/dune-package.t/run.t
+++ b/test/blackbox-tests/test-cases/dune-package.t/run.t
@@ -46,7 +46,6 @@
    (kind normal)
    (archives (byte byte_only/d.cma))
    (plugins (byte byte_only/d.cma))
-   (native_archives byte_only/d$ext_lib)
    (main_module_name D)
    (modes byte)
    (modules