diff --git a/src/bootstrap/doc.rs b/src/bootstrap/doc.rs
index 31eda2dc984..eb29a5e9ffc 100644
--- a/src/bootstrap/doc.rs
+++ b/src/bootstrap/doc.rs
@@ -643,7 +643,7 @@ fn run(self, builder: &Builder<'_>) {
 }
 
 macro_rules! tool_doc {
-    ($tool: ident, $should_run: literal, $path: literal, [$($krate: literal),+ $(,)?] $(,)?) => {
+    ($tool: ident, $should_run: literal, $path: literal, [$($krate: literal),+ $(,)?], in_tree = $in_tree:expr $(,)?) => {
         #[derive(Debug, Copy, Clone, Hash, PartialEq, Eq)]
         pub struct $tool {
             target: TargetSelection,
@@ -699,6 +699,12 @@ fn run(self, builder: &Builder<'_>) {
                 t!(fs::create_dir_all(&out_dir));
                 t!(symlink_dir_force(&builder.config, &out, &out_dir));
 
+                let source_type = if $in_tree == true {
+                    SourceType::InTree
+                } else {
+                    SourceType::Submodule
+                };
+
                 // Build cargo command.
                 let mut cargo = prepare_tool_cargo(
                     builder,
@@ -707,7 +713,7 @@ fn run(self, builder: &Builder<'_>) {
                     target,
                     "doc",
                     $path,
-                    SourceType::InTree,
+                    source_type,
                     &[],
                 );
 
@@ -729,15 +735,22 @@ fn run(self, builder: &Builder<'_>) {
     }
 }
 
-tool_doc!(Rustdoc, "rustdoc-tool", "src/tools/rustdoc", ["rustdoc", "rustdoc-json-types"]);
+tool_doc!(
+    Rustdoc,
+    "rustdoc-tool",
+    "src/tools/rustdoc",
+    ["rustdoc", "rustdoc-json-types"],
+    in_tree = true
+);
 tool_doc!(
     Rustfmt,
     "rustfmt-nightly",
     "src/tools/rustfmt",
     ["rustfmt-nightly", "rustfmt-config_proc_macro"],
+    in_tree = true
 );
-tool_doc!(Clippy, "clippy", "src/tools/clippy", ["clippy_utils"]);
-tool_doc!(Miri, "miri", "src/tools/miri", ["miri"]);
+tool_doc!(Clippy, "clippy", "src/tools/clippy", ["clippy_utils"], in_tree = true);
+tool_doc!(Miri, "miri", "src/tools/miri", ["miri"], in_tree = false);
 
 #[derive(Ord, PartialOrd, Debug, Copy, Clone, Hash, PartialEq, Eq)]
 pub struct ErrorIndex {