diff --git a/lib/mix/lib/mix/tasks/clean.ex b/lib/mix/lib/mix/tasks/clean.ex
index b0dcf4c6e8c..41d6dc75472 100644
--- a/lib/mix/lib/mix/tasks/clean.ex
+++ b/lib/mix/lib/mix/tasks/clean.ex
@@ -57,6 +57,22 @@ defmodule Mix.Tasks.Clean do
       |> Path.join("*#{opts[:only]}")
 
     if opts[:deps] do
+      deps_path = Mix.Project.deps_path()
+      build_lib = Path.join(build, "lib")
+      loaded_deps = Mix.Dep.Converger.converge([])
+
+      apps =
+        build_lib
+        |> Path.join("*")
+        |> Path.wildcard()
+        |> Enum.filter(&File.dir?/1)
+        |> Enum.map(&Path.basename/1)
+        |> Enum.reject(&(&1 == to_string(Mix.Project.config()[:app])))
+
+      Mix.Project.with_deps_lock(fn ->
+        Mix.Tasks.Deps.Clean.clean_generated_sources(apps, build_lib, deps_path, loaded_deps)
+      end)
+
       build
       |> Path.wildcard()
       |> Enum.each(&File.rm_rf/1)
diff --git a/lib/mix/lib/mix/tasks/deps.clean.ex b/lib/mix/lib/mix/tasks/deps.clean.ex
index 5e59334c80a..0d450724f51 100644
--- a/lib/mix/lib/mix/tasks/deps.clean.ex
+++ b/lib/mix/lib/mix/tasks/deps.clean.ex
@@ -68,6 +68,7 @@ defmodule Mix.Tasks.Deps.Clean do
       end
 
     Mix.Project.with_build_lock(fn ->
+      clean_generated_sources(apps_to_clean, build_path, deps_path, loaded_deps)
       clean_build(apps_to_clean, build_path)
     end)
 
@@ -118,6 +119,60 @@ defmodule Mix.Tasks.Deps.Clean do
     end
   end
 
+  # Called from Mix.Tasks.Clean for --deps mode.
+  @doc false
+  def clean_generated_sources([], _build_path, _deps_path, _loaded_deps), do: :ok
+
+  def clean_generated_sources([app | rest], build_path, deps_path, loaded_deps) do
+    dest =
+      case Enum.find(loaded_deps, &(Atom.to_string(&1.app) == app)) do
+        %{opts: opts} -> opts[:dest]
+        nil -> Path.expand(Path.join(deps_path, app))
+      end
+
+    # When no Mix manifests exist (e.g. rebar3 deps compiled externally),
+    # infer generated files from co-located .yrl/.xrl sources.
+    paths =
+      case get_manifest_paths(build_path, app) do
+        [] ->
+          erl_paths_from_grammar_sources(dest)
+
+        manifest_paths ->
+          manifest_paths
+      end
+
+    maybe_remove_files(paths, dest)
+
+    clean_generated_sources(rest, build_path, deps_path, loaded_deps)
+  end
+
+  defp maybe_remove_files(paths, dest) do
+    paths
+    |> Enum.uniq()
+    |> Enum.map(&Path.expand(&1, dest))
+    |> Enum.filter(&String.starts_with?(&1, dest <> "/"))
+    |> Enum.each(fn expanded ->
+      case File.rm(expanded) do
+        :ok -> :ok
+        {:error, reason} -> maybe_warn_failed_file_deletion({:error, reason, expanded})
+      end
+    end)
+  end
+
+  defp erl_paths_from_grammar_sources(dest) do
+    ~w[yrl xrl]
+    |> Enum.flat_map(&Path.wildcard(Path.join([dest, "**", "*.#{&1}"])))
+    |> Enum.map(&(Path.rootname(&1) <> ".erl"))
+  end
+
+  defp get_manifest_paths(build_path, app) do
+    build_path
+    |> Path.join(to_string(app))
+    |> Path.wildcard()
+    |> Enum.flat_map(&Path.wildcard(Path.join(&1, ".mix/compile.{yecc,leex}")))
+    |> Enum.flat_map(&Mix.Compilers.Erlang.outputs/1)
+  end
+
   defp clean_build(apps, build_path) do
     shell = Mix.shell()
 
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/mix.exs b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/mix.exs
new file mode 100644
index 00000000000..46cf84a7a2c
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/mix.exs
@@ -0,0 +1,4 @@
+defmodule ParserDep.MixProject do
+  use Mix.Project
+  def project, do: [app: :parser_dep, version: "0.1.0"]
+end
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/handwritten.erl b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/handwritten.erl
new file mode 100644
index 00000000000..e387885cf31
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/handwritten.erl
@@ -0,0 +1,4 @@
+%% Hand-authored — NOT generated, must never be removed by mix clean.
+-module(handwritten).
+-export([run/0]).
+run() -> ok.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.erl b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.erl
new file mode 100644
index 00000000000..a9c146678f2
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.erl
@@ -0,0 +1,4 @@
+%% Generated by leex from lexer.xrl — this file should be removed by mix clean.
+-module(lexer).
+-export([string/1]).
+string(_) -> ok.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.xrl b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.xrl
new file mode 100644
index 00000000000..4b2e7d07d3d
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/lexer.xrl
@@ -0,0 +1,5 @@
+Definitions.
+D = [0-9]
+Rules.
+{D}+ : {token, {number, TokenLine, list_to_integer(TokenChars)}}.
+Erlang code.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.erl b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.erl
new file mode 100644
index 00000000000..a8154fc421f
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.erl
@@ -0,0 +1,4 @@
+%% Generated by yecc from parser.yrl — this file should be removed by mix clean.
+-module(parser).
+-export([parse/1]).
+parse(_) -> ok.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.yrl b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.yrl
new file mode 100644
index 00000000000..84bd1908714
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/parser_dep/src/parser.yrl
@@ -0,0 +1,4 @@
+Nonterminals expr.
+Terminals number.
+Rootsymbol expr.
+expr -> number : '$1'.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/rebar.config b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/rebar.config
new file mode 100644
index 00000000000..9fba03ceb84
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/rebar.config
@@ -0,0 +1 @@
+{erl_opts, []}.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.erl b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.erl
new file mode 100644
index 00000000000..57c8c064939
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.erl
@@ -0,0 +1,4 @@
+%% Generated by yecc from rb_parser.yrl — this file should be removed by mix clean.
+-module(rb_parser).
+-export([parse/1]).
+parse(_) -> ok.
diff --git a/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.yrl b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.yrl
new file mode 100644
index 00000000000..84bd1908714
--- /dev/null
+++ b/lib/mix/test/fixtures/clean_with_yecc/deps/rebar_dep/src/rb_parser.yrl
@@ -0,0 +1,4 @@
+Nonterminals expr.
+Terminals number.
+Rootsymbol expr.
+expr -> number : '$1'.
diff --git a/lib/mix/test/mix/tasks/clean_test.exs b/lib/mix/test/mix/tasks/clean_test.exs
index 3af7d79328f..b8f678b8bf2 100644
--- a/lib/mix/test/mix/tasks/clean_test.exs
+++ b/lib/mix/test/mix/tasks/clean_test.exs
@@ -53,6 +53,81 @@ defmodule Mix.Tasks.CleanTest do
     end)
   end
 
+  defmodule ParserOnly do
+    def project do
+      [
+        app: :clean_with_yecc,
+        version: "0.1.0",
+        deps: [{:parser_dep, path: "deps/parser_dep"}]
+      ]
+    end
+  end
+
+  defp yecc_manifest(build_dir, relative_paths) do
+    write_manifest(build_dir, "compile.yecc", relative_paths)
+  end
+
+  defp leex_manifest(build_dir, relative_paths) do
+    write_manifest(build_dir, "compile.leex", relative_paths)
+  end
+
+  defp write_manifest(build_dir, name, relative_paths) do
+    mix_dir = Path.join(build_dir, ".mix")
+    File.mkdir_p!(mix_dir)
+    entries = Enum.map(relative_paths, &{&1, []})
+    File.write!(Path.join(mix_dir, name), :erlang.term_to_binary({1, entries}))
+  end
+
+  test "--deps removes yecc-generated .erl files from dep source" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+
+      build_dir = "_build/dev/lib/parser_dep"
+      File.mkdir_p!(Path.join(build_dir, "ebin"))
+      yecc_manifest(build_dir, ["src/parser.erl"])
+
+      Mix.Tasks.Clean.run(["--deps"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+      refute File.exists?("_build/dev")
+    end)
+  end
+
+  test "without --deps does not touch dep generated files" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+
+      Mix.Tasks.Clean.run([])
+
+      assert File.exists?("deps/parser_dep/src/parser.erl")
+    end)
+  end
+
+  test "--deps --only dev scopes generated-file cleanup to dev environment" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+
+      dev_dir = "_build/dev/lib/parser_dep"
+      test_dir = "_build/test/lib/parser_dep"
+
+      File.mkdir_p!(Path.join(dev_dir, "ebin"))
+      File.mkdir_p!(Path.join(test_dir, "ebin"))
+
+      # dev tracks parser.erl; test tracks lexer.erl
+      yecc_manifest(dev_dir, ["src/parser.erl"])
+      leex_manifest(test_dir, ["src/lexer.erl"])
+
+      Mix.Tasks.Clean.run(["--deps", "--only", "dev"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      # test manifest was not processed
+      assert File.exists?("deps/parser_dep/src/lexer.erl")
+      refute File.exists?("_build/dev")
+      assert File.exists?("_build/test")
+    end)
+  end
+
   test "invokes compiler hook defined in project" do
     Mix.ProjectStack.post_config(compilers: Mix.compilers() ++ [:testc])
 
diff --git a/lib/mix/test/mix/tasks/deps.clean_test.exs b/lib/mix/test/mix/tasks/deps.clean_test.exs
new file mode 100644
index 00000000000..c8ac393af03
--- /dev/null
+++ b/lib/mix/test/mix/tasks/deps.clean_test.exs
@@ -0,0 +1,261 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: 2021 The Elixir Team
+
+Code.require_file("../../test_helper.exs", __DIR__)
+
+defmodule Mix.Tasks.Deps.CleanTest do
+  use MixTest.Case
+
+  # Project with both a Mix dep (parser_dep) and a rebar3 dep (rebar_dep).
+  # Both use path: so they are available without network access in tests.
+  defmodule BothDeps do
+    def project do
+      [
+        app: :clean_with_yecc,
+        version: "0.1.0",
+        deps: [
+          {:parser_dep, path: "deps/parser_dep"},
+          {:rebar_dep, path: "deps/rebar_dep"}
+        ]
+      ]
+    end
+  end
+
+  defmodule ParserOnly do
+    def project do
+      [
+        app: :clean_with_yecc,
+        version: "0.1.0",
+        deps: [{:parser_dep, path: "deps/parser_dep"}]
+      ]
+    end
+  end
+
+  # Writes a compile.yecc manifest exactly as the real compiler does:
+  # relative paths from the dep's working directory, version tag 1.
+  defp yecc_manifest(build_dir, relative_paths) do
+    write_manifest(build_dir, "compile.yecc", relative_paths)
+  end
+
+  defp leex_manifest(build_dir, relative_paths) do
+    write_manifest(build_dir, "compile.leex", relative_paths)
+  end
+
+  defp write_manifest(build_dir, name, relative_paths) do
+    mix_dir = Path.join(build_dir, ".mix")
+    File.mkdir_p!(mix_dir)
+    entries = Enum.map(relative_paths, &{&1, []})
+    File.write!(Path.join(mix_dir, name), :erlang.term_to_binary({1, entries}))
+  end
+
+  defp touch_build(app) do
+    dir = "_build/dev/lib/#{app}"
+    File.mkdir_p!(Path.join(dir, "ebin"))
+
+    File.write!(
+      Path.join([dir, "ebin", "#{app}.app"]),
+      "{application, #{app}, [{vsn,\"0.1.0\"}]}."
+    )
+
+    dir
+  end
+
+  test "removes yecc-generated .erl, preserves .yrl source" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      yecc_manifest(build_dir, ["src/parser.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+    end)
+  end
+
+  test "removes leex-generated .erl, preserves .xrl source" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      leex_manifest(build_dir, ["src/lexer.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/lexer.erl")
+      assert File.exists?("deps/parser_dep/src/lexer.xrl")
+    end)
+  end
+
+  test "hand-written .erl not tracked in any manifest is never deleted" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      # manifest only tracks parser.erl — handwritten.erl is NOT listed
+      yecc_manifest(build_dir, ["src/parser.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      assert File.exists?("deps/parser_dep/src/handwritten.erl")
+    end)
+  end
+
+  test "cleans both yecc and leex generated files in one pass" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      yecc_manifest(build_dir, ["src/parser.erl"])
+      leex_manifest(build_dir, ["src/lexer.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      refute File.exists?("deps/parser_dep/src/lexer.erl")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+      assert File.exists?("deps/parser_dep/src/lexer.xrl")
+    end)
+  end
+
+  test "generated .erl in non-standard source directory is deleted" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      # dep uses erlc_paths: ["grammar"] instead of the default "src"
+      File.mkdir_p!("deps/parser_dep/grammar")
+      File.write!("deps/parser_dep/grammar/dialect.erl", "-module(dialect).")
+      yecc_manifest(build_dir, ["grammar/dialect.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/grammar/dialect.erl")
+    end)
+  end
+
+  test "--build still removes generated source files, leaves dep directory" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      yecc_manifest(build_dir, ["src/parser.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["--build", "parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      # --build keeps the dep source directory intact
+      assert File.dir?("deps/parser_dep")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+    end)
+  end
+
+  test "--all --build removes generated files from every dep" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(BothDeps)
+      parser_build = touch_build(:parser_dep)
+      rebar_build = touch_build(:rebar_dep)
+      yecc_manifest(parser_build, ["src/parser.erl"])
+      yecc_manifest(rebar_build, ["src/rb_parser.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["--all", "--build"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      refute File.exists?("deps/rebar_dep/src/rb_parser.erl")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+      assert File.exists?("deps/rebar_dep/src/rb_parser.yrl")
+    end)
+  end
+
+  test "manifests in multiple envs point to same .erl — Enum.uniq deduplicates before deletion" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+
+      for env <- ["dev", "test"] do
+        dir = "_build/#{env}/lib/parser_dep"
+        File.mkdir_p!(Path.join(dir, "ebin"))
+        yecc_manifest(dir, ["src/parser.erl"])
+      end
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+    end)
+  end
+
+  test "--only scopes manifest reading to the specified environment" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+
+      dev_dir = "_build/dev/lib/parser_dep"
+      test_dir = "_build/test/lib/parser_dep"
+
+      for dir <- [dev_dir, test_dir] do
+        File.mkdir_p!(Path.join(dir, "ebin"))
+      end
+
+      # dev tracks src/parser.erl; test tracks src/lexer.erl
+      yecc_manifest(dev_dir, ["src/parser.erl"])
+      leex_manifest(test_dir, ["src/lexer.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep", "--only", "dev"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      # test manifest was not processed
+      assert File.exists?("deps/parser_dep/src/lexer.erl")
+    end)
+  end
+
+  test "rebar3 dep: deletes .erl files inferred from co-located .yrl/.xrl when no manifests exist" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(BothDeps)
+      # No build dir created for rebar_dep — rebar3 never writes Mix manifests.
+      # The fixture has src/rb_parser.yrl and src/rb_parser.erl pre-populated.
+
+      Mix.Tasks.Deps.Clean.run(["rebar_dep"])
+
+      refute File.exists?("deps/rebar_dep/src/rb_parser.erl")
+      assert File.exists?("deps/rebar_dep/src/rb_parser.yrl")
+    end)
+  end
+
+  test "dep with no manifests removes .erl files inferred from .yrl/.xrl sources" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      # no _build at all — dep was never compiled by Mix
+      # parser.erl/lexer.erl are inferred from parser.yrl/lexer.xrl and deleted
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      refute File.exists?("deps/parser_dep/src/parser.erl")
+      refute File.exists?("deps/parser_dep/src/lexer.erl")
+      assert File.exists?("deps/parser_dep/src/parser.yrl")
+      assert File.exists?("deps/parser_dep/src/lexer.xrl")
+      # hand-written .erl with no grammar counterpart is preserved
+      assert File.exists?("deps/parser_dep/src/handwritten.erl")
+    end)
+  end
+
+  test "idempotent: running deps.clean twice does not error" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      yecc_manifest(build_dir, ["src/parser.erl"])
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+      # parser.erl is now gone and _build deleted; second run must not raise
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+      # the second run warns that the dep is not in the build directory
+      assert_received {:mix_shell, :error, ["warning: the dependency parser_dep " <> _]}
+    end)
+  end
+
+  test "does not delete a file whose expanded path escapes the dep source root" do
+    in_fixture("clean_with_yecc", fn ->
+      Mix.Project.push(ParserOnly)
+      build_dir = touch_build(:parser_dep)
+      # A hypothetical manifest entry with path traversal
+      write_manifest(build_dir, "compile.yecc", ["../../some_other_file.erl"])
+      File.write!("some_other_file.erl", "not to be deleted")
+
+      Mix.Tasks.Deps.Clean.run(["parser_dep"])
+
+      assert File.exists?("some_other_file.erl")
+    end)
+  end
+end