diff --git a/pkgs/development/ocaml-modules/ocaml-freestanding/default.nix b/pkgs/development/ocaml-modules/ocaml-freestanding/default.nix
index cf72397057d..942d69e5919 100644
--- a/pkgs/development/ocaml-modules/ocaml-freestanding/default.nix
+++ b/pkgs/development/ocaml-modules/ocaml-freestanding/default.nix
@@ -22,13 +22,13 @@ else
 stdenv.mkDerivation rec {
   name = "ocaml${ocaml.version}-${pname}-${version}";
   inherit pname;
-  version = "0.6.4";
+  version = "0.6.5";
 
   src = fetchFromGitHub {
     owner = "mirage";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0w3x2wfd04qr6mci4cp1gfqw33yysp8gamgkpgbgwslr0skryiq5";
+    sha256 = "sha256:1mbyjzwcs64n7i3xkkyaxgl3r46drbl0gkqf3fqgm2kh3q03638l";
   };
 
   postUnpack = ''
@@ -55,15 +55,6 @@ stdenv.mkDerivation rec {
     runHook postConfigure
   '';
 
-  preBuild = ''
-    # perform substitutions, so opam isn't needed
-    for flags in flags/cflags.tmp flags/libs.tmp; do
-      substitute "$flags.in" "$flags" \
-        --replace "%{prefix}%" "$out" \
-        --replace "%{ocaml-freestanding:lib}%" "$out/lib"
-    done
-  '';
-
   installPhase = ''
     runHook preInstall
     ./install.sh "$out"
diff --git a/pkgs/development/ocaml-modules/ocaml-freestanding/no-opam.patch b/pkgs/development/ocaml-modules/ocaml-freestanding/no-opam.patch
index 43141b1472a..45f271ec0f2 100644
--- a/pkgs/development/ocaml-modules/ocaml-freestanding/no-opam.patch
+++ b/pkgs/development/ocaml-modules/ocaml-freestanding/no-opam.patch
@@ -22,43 +22,6 @@ Date:   Thu Mar 18 01:07:49 2021 +0100
     nice bonus). The Makefile needs no fix since the target ocaml/Makefile
     won't be built if it's already present.
 
-diff --git a/Makefile b/Makefile
-index b07b8c6..a68b31d 100644
---- a/Makefile
-+++ b/Makefile
-@@ -2,6 +2,12 @@
- 
- include Makeconf
- 
-+ifneq ($(shell command -v opam),)
-+	# only set if opam is available and PKG_CONFIG_PATH isn't
-+	# already set in the environment or on the command line
-+	PKG_CONFIG_PATH ?= $(shell opam config var prefix)/lib/pkgconfig
-+endif
-+
- FREESTANDING_LIBS=openlibm/libopenlibm.a \
- 		  ocaml/runtime/libasmrun.a \
- 		  nolibc/libnolibc.a
-@@ -73,8 +79,7 @@ flags/libs.tmp: flags/libs.tmp.in
- 	opam config subst $@
- 
- flags/libs: flags/libs.tmp Makeconf
--	env PKG_CONFIG_PATH="$(shell opam config var prefix)/lib/pkgconfig" \
--	    pkg-config $(PKG_CONFIG_DEPS) --libs >> $<
-+	pkg-config $(PKG_CONFIG_DEPS) --libs >> $<
- 	awk -v RS= -- '{ \
- 	    sub("@@PKG_CONFIG_EXTRA_LIBS@@", "$(PKG_CONFIG_EXTRA_LIBS)", $$0); \
- 	    print "(", $$0, ")" \
-@@ -84,8 +89,7 @@ flags/cflags.tmp: flags/cflags.tmp.in
- 	opam config subst $@
- 
- flags/cflags: flags/cflags.tmp Makeconf
--	env PKG_CONFIG_PATH="$(shell opam config var prefix)/lib/pkgconfig" \
--	    pkg-config $(PKG_CONFIG_DEPS) --cflags >> $<
-+	pkg-config $(PKG_CONFIG_DEPS) --cflags >> $<
- 	awk -v RS= -- '{ \
- 	    print "(", $$0, ")" \
- 	    }' $< >$@
 diff --git a/configure.sh b/configure.sh
 index 4d154ed..c254f7b 100755
 --- a/configure.sh