diff --git a/src/bootstrap/builder.rs b/src/bootstrap/builder.rs
index 8d999302a6d7b..251431a15eb89 100644
--- a/src/bootstrap/builder.rs
+++ b/src/bootstrap/builder.rs
@@ -1094,7 +1094,13 @@ impl<'a> Builder<'a> {
             let my_out = match mode {
                 // This is the intended out directory for compiler documentation.
                 Mode::Rustc | Mode::ToolRustc => self.compiler_doc_out(target),
-                Mode::Std => out_dir.join(target.triple).join("doc"),
+                Mode::Std => {
+                    if self.config.cmd.json() {
+                        out_dir.join(target.triple).join("json-doc")
+                    } else {
+                        out_dir.join(target.triple).join("doc")
+                    }
+                }
                 _ => panic!("doc mode {:?} not expected", mode),
             };
             let rustdoc = self.rustdoc(compiler);
diff --git a/src/bootstrap/doc.rs b/src/bootstrap/doc.rs
index 3180a12c85be7..571396eb835bf 100644
--- a/src/bootstrap/doc.rs
+++ b/src/bootstrap/doc.rs
@@ -564,27 +564,22 @@ fn doc_std(
         );
     }
     let compiler = builder.compiler(stage, builder.config.build);
+
+    let target_doc_dir_name = if format == DocumentationFormat::JSON { "json-doc" } else { "doc" };
+    let target_dir =
+        builder.stage_out(compiler, Mode::Std).join(target.triple).join(target_doc_dir_name);
+
     // This is directory where the compiler will place the output of the command.
     // We will then copy the files from this directory into the final `out` directory, the specified
     // as a function parameter.
-    let out_dir = builder.stage_out(compiler, Mode::Std).join(target.triple).join("doc");
-    // `cargo` uses the same directory for both JSON docs and HTML docs.
-    // This could lead to cross-contamination when copying files into the specified `out` directory.
-    // For example:
-    // ```bash
-    // x doc std
-    // x doc std --json
-    // ```
-    // could lead to HTML docs being copied into the JSON docs output directory.
-    // To avoid this issue, we clean the doc folder before invoking `cargo`.
-    if out_dir.exists() {
-        builder.remove_dir(&out_dir);
-    }
+    let out_dir = target_dir.join(target.triple).join("doc");
 
     let run_cargo_rustdoc_for = |package: &str| {
         let mut cargo = builder.cargo(compiler, Mode::Std, SourceType::InTree, target, "rustdoc");
         compile::std_cargo(builder, target, compiler.stage, &mut cargo);
         cargo
+            .arg("--target-dir")
+            .arg(&*target_dir.to_string_lossy())
             .arg("-p")
             .arg(package)
             .arg("-Zskip-rustdoc-fingerprint")
diff --git a/src/test/run-make/rustdoc-verify-output-files/Makefile b/src/test/run-make/rustdoc-verify-output-files/Makefile
new file mode 100644
index 0000000000000..bfabbbc65862f
--- /dev/null
+++ b/src/test/run-make/rustdoc-verify-output-files/Makefile
@@ -0,0 +1,36 @@
+include ../../run-make-fulldeps/tools.mk
+
+OUTPUT_DIR := "$(TMPDIR)/rustdoc"
+TMP_OUTPUT_DIR := "$(TMPDIR)/tmp-rustdoc"
+
+all:
+	# Generate html docs
+	$(RUSTDOC) src/lib.rs --crate-name foobar --crate-type lib --out-dir $(OUTPUT_DIR)
+
+	# Copy first output for to check if it's exactly same after second compilation
+	cp -R $(OUTPUT_DIR) $(TMP_OUTPUT_DIR)
+
+	# Generate html docs once again on same output
+	$(RUSTDOC) src/lib.rs --crate-name foobar --crate-type lib --out-dir $(OUTPUT_DIR)
+
+	# Check if everything exactly same
+	$(DIFF) -r -q $(OUTPUT_DIR) $(TMP_OUTPUT_DIR)
+
+	# Generate json doc on the same output
+	$(RUSTDOC) src/lib.rs --crate-name foobar --crate-type lib --out-dir $(OUTPUT_DIR) -Z unstable-options --output-format json
+
+	# Check if expected json file is generated
+	[ -e $(OUTPUT_DIR)/foobar.json ]
+
+	# TODO
+	# We should re-generate json doc once again and compare the diff with previously
+	# generated one. Because layout of json docs changes in each compilation, we can't
+	# do that currently.
+	#
+	# See https://github.com/rust-lang/rust/issues/103785#issuecomment-1307425590 for details.
+
+	# remove generated json doc
+	rm $(OUTPUT_DIR)/foobar.json
+
+	# Check if json doc compilation broke any of the html files generated previously
+	$(DIFF) -r -q $(OUTPUT_DIR) $(TMP_OUTPUT_DIR)
diff --git a/src/test/run-make/rustdoc-verify-output-files/src/lib.rs b/src/test/run-make/rustdoc-verify-output-files/src/lib.rs
new file mode 100644
index 0000000000000..5df7576133a68
--- /dev/null
+++ b/src/test/run-make/rustdoc-verify-output-files/src/lib.rs
@@ -0,0 +1 @@
+// nothing to see here