diff --git a/modules/home-manager/programs/nix-index/module.nix b/modules/home-manager/programs/nix-index/module.nix
index a1ca372..f43281b 100644
--- a/modules/home-manager/programs/nix-index/module.nix
+++ b/modules/home-manager/programs/nix-index/module.nix
@@ -10,11 +10,14 @@ in {
   options.my.programs.nix-index = {
     enable = lib.mkDefaultEnableOption "nix-index";
     package = lib.mkOption {
-      default = pkgs.nix-index;
-      defaultText = "pkgs.nix-index";
-      description = ''
-        The nix-index package to use.
-      '';
+      default = pkgs.nix-index.override (prev: {
+        nix-index-unwrapped = prev.nix-index-unwrapped.overrideAttrs (prevAttrs: {
+          patches = (prevAttrs.patches or []) ++ [
+            # https://github.com/nix-community/nix-index/pull/243
+            ./skip-fhs-by-default.patch
+          ];
+        });
+      });
 
       type = with lib.types; package;
     };
@@ -24,6 +27,8 @@ in {
     my.persist.directories = [ "~/.cache/nix-index" ];
 
     programs.command-not-found.enable = lib.mkForce false;
-    programs.nix-index.enable = true;
+    programs.nix-index = {
+      inherit (cfg) enable package;
+    };
   };
 }
diff --git a/modules/home-manager/programs/nix-index/skip-fhs-by-default.patch b/modules/home-manager/programs/nix-index/skip-fhs-by-default.patch
new file mode 100644
index 0000000..b357366
--- /dev/null
+++ b/modules/home-manager/programs/nix-index/skip-fhs-by-default.patch
@@ -0,0 +1,51 @@
+diff --git a/CHANGELOG.md b/CHANGELOG.md
+index 3c09c04..25f62e8 100644
+--- a/CHANGELOG.md
++++ b/CHANGELOG.md
+@@ -3,6 +3,8 @@
+ ### Fixed
+ ### Changed
+
++* `--top-level` is now the default. To use the old default, add `--all`.
++
+ ## 0.1.8
+ ### Added
+
+diff --git a/command-not-found.sh b/command-not-found.sh
+index 5f30bad..64457ef 100755
+--- a/command-not-found.sh
++++ b/command-not-found.sh
+@@ -16,7 +16,7 @@ command_not_found_handle () {
+
+     toplevel=nixpkgs # nixpkgs should always be available even in NixOS
+     cmd=$1
+-    attrs=$(@out@/bin/nix-locate --minimal --no-group --type x --type s --top-level --whole-name --at-root "/bin/$cmd")
++    attrs=$(@out@/bin/nix-locate --minimal --no-group --type x --type s --whole-name --at-root "/bin/$cmd")
+     len=$(echo -n "$attrs" | grep -c "^")
+
+     case $len in
+diff --git a/src/bin/nix-locate.rs b/src/bin/nix-locate.rs
+index 760d398..2c18747 100644
+--- a/src/bin/nix-locate.rs
++++ b/src/bin/nix-locate.rs
+@@ -187,7 +187,7 @@ fn process_args(matches: Opts) -> result::Result<Args, clap::Error> {
+         file_type: matches
+             .r#type
+             .unwrap_or_else(|| files::ALL_FILE_TYPES.to_vec()),
+-        only_toplevel: matches.top_level,
++        only_toplevel: !matches.all,
+         color,
+         minimal: matches.minimal,
+     };
+@@ -255,9 +255,9 @@ struct Opts {
+     #[clap(long, name = "HASH")]
+     hash: Option<String>,
+
+-    /// Only print matches from packages that show up in `nix-env -qa`.
++    /// Print all matches, not only print from packages that show up in `nix-env -qa`.
+     #[clap(long)]
+-    top_level: bool,
++    all: bool,
+
+     /// Only print matches for files that have this type. If the option is given multiple times,
+     /// a file will be printed if it has any of the given types.