diff --git a/pkgs/build-support/setup-hooks/make-symlinks-relative.sh b/pkgs/build-support/setup-hooks/make-symlinks-relative.sh
index f34353a7617b..b07b0c5ae804 100644
--- a/pkgs/build-support/setup-hooks/make-symlinks-relative.sh
+++ b/pkgs/build-support/setup-hooks/make-symlinks-relative.sh
@@ -1,4 +1,6 @@
-postFixupHooks+=(_makeSymlinksRelative)
+# symlinks are often created in postFixup
+# don't use fixupOutputHooks, it is before postFixup
+postFixupHooks+=(_makeSymlinksRelativeInAllOutputs)
 
 # For every symlink in $output that refers to another file in $output
 # ensure that the symlink is relative. This removes references to the output
@@ -26,3 +28,10 @@ _makeSymlinksRelative() {
 
     done < <(find $prefix -type l -print0)
 }
+
+_makeSymlinksRelativeInAllOutputs() {
+  local output
+  for output in $(getAllOutputNames); do
+    prefix="${!output}" _makeSymlinksRelative
+  done
+}
diff --git a/pkgs/test/stdenv/hooks.nix b/pkgs/test/stdenv/hooks.nix
index 7f25d7dbd2db..3d72efae6c47 100644
--- a/pkgs/test/stdenv/hooks.nix
+++ b/pkgs/test/stdenv/hooks.nix
@@ -23,19 +23,29 @@
     };
   make-symlinks-relative = stdenv.mkDerivation {
     name = "test-make-symlinks-relative";
+    outputs = [ "out" "man" ];
     buildCommand = ''
       mkdir -p $out/{bar,baz}
+      mkdir -p $man/share/{x,y}
       source1="$out/bar/foo"
       destination1="$out/baz/foo"
+      source2="$man/share/x/file1"
+      destination2="$man/share/y/file2"
       echo foo > $source1
+      echo foo > $source2
       ln -s $source1 $destination1
+      ln -s $source2 $destination2
       echo "symlink before patching: $(readlink $destination1)"
+      echo "symlink before patching: $(readlink $destination2)"
 
-      _makeSymlinksRelative
+      _makeSymlinksRelativeInAllOutputs
 
       echo "symlink after patching: $(readlink $destination1)"
       ([[ -e $destination1 ]] && echo "symlink isn't broken") || (echo "symlink is broken" && exit 1)
       ([[ $(readlink $destination1) == "../bar/foo" ]] && echo "absolute symlink was made relative") || (echo "symlink was not made relative" && exit 1)
+      echo "symlink after patching: $(readlink $destination2)"
+      ([[ -e $destination2 ]] && echo "symlink isn't broken") || (echo "symlink is broken" && exit 1)
+      ([[ $(readlink $destination2) == "../x/file1" ]] && echo "absolute symlink was made relative") || (echo "symlink was not made relative" && exit 1)
     '';
   };
   move-docs = stdenv.mkDerivation {