diff --git a/apps/rebar/src/rebar_prv_clean.erl b/apps/rebar/src/rebar_prv_clean.erl
index 71a8066c3..010d67cad 100644
--- a/apps/rebar/src/rebar_prv_clean.erl
+++ b/apps/rebar/src/rebar_prv_clean.erl
@@ -12,7 +12,7 @@
 -include("rebar.hrl").
 
 -define(PROVIDER, clean).
--define(DEPS, [app_discovery, install_deps]).
+-define(DEPS, []).
 
 %% ===================================================================
 %% Public API
@@ -37,7 +37,16 @@ do(State) ->
     Providers = rebar_state:providers(State),
     {All, Profiles, Specific} = handle_args(State),
 
-    State1 = rebar_state:apply_profiles(State, [list_to_atom(X) || X <- Profiles]),
+    %% Invoke provider deps as the desired profile(s) so the discovery of
+    %% apps respects profile options.
+    Task = if All; Specific =/= [] -> "install_deps";
+              true -> "app_discovery"
+           end,
+    State0 = rebar_state:command_args(
+        State,
+        lists:join(",", ["default"|Profiles]) ++ [Task]
+    ),
+    {ok, State1} = rebar_prv_as:do(State0),
 
     Cwd = rebar_dir:get_cwd(),
     rebar_hooks:run_all_hooks(Cwd, pre, ?PROVIDER, Providers, State1),
@@ -45,7 +54,14 @@ do(State) ->
     if All; Specific =/= [] ->
         DepsDir = rebar_dir:deps_dir(State1),
         DepsDirs = filelib:wildcard(filename:join(DepsDir, "*")),
-        AllApps = rebar_app_discover:find_apps(DepsDirs, all, State),
+        ProjectApps = rebar_state:project_apps(State1),
+        Deps = rebar_state:all_deps(State1),
+        KnownAppNames = [rebar_app_info:name(App) || App <- ProjectApps++Deps],
+        ParsedApps = rebar_app_discover:find_apps(DepsDirs, all, State1),
+        AllApps = ProjectApps ++ Deps ++
+                  [App || App <- ParsedApps,
+                          not lists:member(rebar_app_info:name(App),
+                                           KnownAppNames)],
         Filter = case All of
             true -> fun(_) -> true end;
             false -> fun(AppInfo) -> filter_name(AppInfo, Specific) end
diff --git a/apps/rebar/test/rebar_as_SUITE.erl b/apps/rebar/test/rebar_as_SUITE.erl
index 78ea8aec9..fce1efcd9 100644
--- a/apps/rebar/test/rebar_as_SUITE.erl
+++ b/apps/rebar/test/rebar_as_SUITE.erl
@@ -198,4 +198,5 @@ clean_as_profile(Config) ->
     rebar_test_utils:run_and_check(Config,
                                    [],
                                    ["clean", "-a", "-p", "foo"],
-                                   {ok, [{app, Name, invalid}]}).
+                                   {ok, [{app, Name, invalid}]}),
+    ok.
diff --git a/apps/rebar/test/rebar_hooks_SUITE.erl b/apps/rebar/test/rebar_hooks_SUITE.erl
index bdef11482..b000125c5 100644
--- a/apps/rebar/test/rebar_hooks_SUITE.erl
+++ b/apps/rebar/test/rebar_hooks_SUITE.erl
@@ -166,10 +166,17 @@ deps_clean_hook_namespace(Config) ->
             ]}
         ]}
     ],
+    %% Only detect dependencies when asked to parse them.
+    %% Avoids scanning and fetching them only to clean them.
     rebar_test_utils:run_and_check(
         Config, RebarConfig, ["clean"],
+        {ok, [{dep_not_exist, "some_dep"}]}
+    ),
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["clean", "-a"],
         {ok, [{dep, "some_dep"}]}
-    ).
+    ),
+    ok.
 
 %% Checks that a hook that is defined on an app (not a top level hook of a project with subapps) is run
 eunit_app_hooks(Config) ->