diff --git a/doc/manual/generate-manpage.nix b/doc/manual/generate-manpage.nix
index 705fc0b69..87891fa7a 100644
--- a/doc/manual/generate-manpage.nix
+++ b/doc/manual/generate-manpage.nix
@@ -79,6 +79,10 @@ let
         # Options
 
         ${showOptions details.flags toplevel.flags}
+
+        > **Note**
+        >
+        > See [`man nix.conf`](@docroot@/command-ref/conf-file.md#command-line-flags) for overriding configuration settings with command line flags.
       '';
 
       showOptions = options: commonOptions:
diff --git a/src/libutil/args.cc b/src/libutil/args.cc
index 00281ce6f..8db293762 100644
--- a/src/libutil/args.cc
+++ b/src/libutil/args.cc
@@ -236,6 +236,7 @@ nlohmann::json Args::toJSON()
 
     for (auto & [name, flag] : longFlags) {
         auto j = nlohmann::json::object();
+        if (hiddenCategories.count(flag->category)) continue;
         if (flag->aliases.count(name)) continue;
         if (flag->shortName)
             j["shortName"] = std::string(1, flag->shortName);