diff --git a/dev/_bootstrap-tests.nix b/dev/_bootstrap-tests.nix
index e2d6670..3c3eb92 100644
--- a/dev/_bootstrap-tests.nix
+++ b/dev/_bootstrap-tests.nix
@@ -48,6 +48,36 @@ let
     inputs.flake-parts.url = "github:hercules-ci/flake-parts";
   };
 
+  bootstrap-all = import ./.. (
+    args
+    // {
+      bootstrap = true;
+      modules = { outputs = _: { }; };
+    }
+  );
+
+  bootstrap-selected = import ./.. (
+    args
+    // {
+      bootstrap = [
+        "flake-file"
+        "nixpkgs"
+      ];
+      modules = { outputs = _: { }; };
+    }
+  );
+
+  bootstrap-override = import ./.. (
+    args
+    // {
+      bootstrap = true;
+      modules = {
+        inputs.nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
+        outputs = _: { };
+      };
+    }
+  );
+
   flake-parts-follows = bootstrap {
     inputs.nixpkgs-lib.url = "github:vic/empty-flake";
     inputs.flake-parts.url = "github:hercules-ci/flake-parts";
@@ -84,6 +114,49 @@ let
     '';
   };
 
+  test-bootstrap-all-inputs = pkgs.writeShellApplication {
+    name = "test-bootstrap-all-inputs";
+    runtimeInputs = [
+      (bootstrap-all.flake-file.apps.write-inputs pkgs)
+    ];
+    text = ''
+      write-inputs
+      grep github:vic/import-tree ${outdir}/inputs.nix
+      grep github:vic/flake-file ${outdir}/inputs.nix
+      grep github:hercules-ci/flake-parts ${outdir}/inputs.nix
+      grep nixpkgs-unstable ${outdir}/inputs.nix
+    '';
+  };
+
+  test-bootstrap-selected-inputs = pkgs.writeShellApplication {
+    name = "test-bootstrap-selected-inputs";
+    runtimeInputs = [
+      (bootstrap-selected.flake-file.apps.write-inputs pkgs)
+    ];
+    text = ''
+      write-inputs
+      grep github:vic/flake-file ${outdir}/inputs.nix
+      grep nixpkgs-unstable ${outdir}/inputs.nix
+      if grep github:vic/import-tree ${outdir}/inputs.nix; then
+        exit 1
+      fi
+      if grep github:hercules-ci/flake-parts ${outdir}/inputs.nix; then
+        exit 1
+      fi
+    '';
+  };
+
+  test-bootstrap-input-override = pkgs.writeShellApplication {
+    name = "test-bootstrap-input-override";
+    runtimeInputs = [
+      (bootstrap-override.flake-file.apps.write-inputs pkgs)
+    ];
+    text = ''
+      write-inputs
+      grep github:nixos/nixpkgs/nixos-unstable ${outdir}/inputs.nix
+    '';
+  };
+
   test-npins = pkgs.writeShellApplication {
     name = "test-npins";
     runtimeInputs = [
@@ -246,6 +319,9 @@ pkgs.mkShell {
   buildInputs = [
     test-inputs
     test-flake
+    test-bootstrap-all-inputs
+    test-bootstrap-selected-inputs
+    test-bootstrap-input-override
     test-unflake
     test-npins
     test-npins-schemes
diff --git a/docs/src/content/docs/reference/bootstrap.mdx b/docs/src/content/docs/reference/bootstrap.mdx
index d025aa3..5ec243f 100644
--- a/docs/src/content/docs/reference/bootstrap.mdx
+++ b/docs/src/content/docs/reference/bootstrap.mdx
@@ -46,7 +46,7 @@ The Nix file or directory containing your flake-file module definitions. All `.n
 
 ### `bootstrap`
 
-Include predefined inputs from the built-in `bootstrap.nix`. When set to `true`, all bootstrap inputs are included. When set to a list, only the named inputs are included.
+Include predefined inputs from `modules/bootstrap/inputs.nix`. When set to `true`, all bootstrap inputs are included. When set to a list, only the named inputs are included. These defaults are imported before your modules, so your modules can override them.
 
 - **Type:** `true` | list of input names
 - **Default:** `[]` (none)
diff --git a/modules/bootstrap/default.nix b/modules/bootstrap/default.nix
index 4d8698e..2a8197e 100644
--- a/modules/bootstrap/default.nix
+++ b/modules/bootstrap/default.nix
@@ -1,6 +1,7 @@
 {
   pkgs ? import <nixpkgs> { },
   modules ? [ ],
+  bootstrap ? [ ],
   outdir ? ".",
   inputs ? null,
   outputs ? null,
@@ -20,6 +21,19 @@ let
 
   tree = (import import-tree) modules;
 
+  bootstrapModule =
+    if bootstrap == true then
+      ./inputs.nix
+    else if builtins.isList bootstrap then
+      let
+        allInputs = (import ./inputs.nix { inherit lib; }).flake-file.inputs;
+      in
+      { flake-file.inputs = lib.filterAttrs (name: _: builtins.elem name bootstrap) allInputs; }
+    else if bootstrap == false then
+      { }
+    else
+      throw "flake-file bootstrap must be true, false, or a list of input names";
+
   attrsOpt = lib.mkOption {
     default = { };
     type = lib.types.submodule { freeformType = lib.types.lazyAttrsOf lib.types.unspecified; };
@@ -27,6 +41,7 @@ let
 
   module = {
     imports = [
+      bootstrapModule
       tree
       ./../default.nix
       ./../options