diff --git a/src/rebar_deps.erl b/src/rebar_deps.erl
index 82c5061..15e7594 100644
--- a/src/rebar_deps.erl
+++ b/src/rebar_deps.erl
@@ -68,31 +68,6 @@ preprocess(Config, _) ->
     %% Add available deps to code path
     Config3 = update_deps_code_path(Config2, AvailableDeps),
 
-    %% If skip_deps=true, mark each dep dir as a skip_dir w/ the core so that
-    %% the current command doesn't run on the dep dir. However, pre/postprocess
-    %% WILL run (and we want it to) for transitivity purposes.
-    %%
-    %% Also, if skip_deps=comma,separated,app,list, then only the given
-    %% dependencies are skipped.
-    NewConfig = case rebar_config:get_global(Config3, skip_deps, false) of
-        "true" ->
-            lists:foldl(
-                fun(#dep{dir = Dir}, C) ->
-                        rebar_config:set_skip_dir(C, Dir)
-                end, Config3, AvailableDeps);
-        Apps when is_list(Apps) ->
-            SkipApps = [list_to_atom(App) || App <- string:tokens(Apps, ",")],
-            lists:foldl(
-                fun(#dep{dir = Dir, app = App}, C) ->
-                        case lists:member(App, SkipApps) of
-                            true -> rebar_config:set_skip_dir(C, Dir);
-                            false -> C
-                        end
-                end, Config3, AvailableDeps);
-        _ ->
-            Config3
-    end,
-
     %% Filtering out 'raw' dependencies so that no commands other than
     %% deps-related can be executed on their directories.
     NonRawAvailableDeps = [D || D <- AvailableDeps, not D#dep.is_raw],
@@ -103,13 +78,38 @@ preprocess(Config, _) ->
             %% any other calls to preprocess() for update-deps beyond the
             %% toplevel directory. They aren't actually harmful, but they slow
             %% things down unnecessarily.
-            NewConfig2 = lists:foldl(fun(D, Acc) ->
+            NewConfig = lists:foldl(fun(D, Acc) ->
                                              rebar_config:set_skip_dir(Acc, D#dep.dir)
-                                     end, NewConfig, collect_deps(rebar_utils:get_cwd(),NewConfig)),
+                                     end, Config3, collect_deps(rebar_utils:get_cwd(), Config3)),
             %% Return the empty list, as we don't want anything processed before
             %% us.
-            {ok, NewConfig2, []};
+            {ok, NewConfig, []};
         _ ->
+            %% If skip_deps=true, mark each dep dir as a skip_dir w/ the core so that
+            %% the current command doesn't run on the dep dir. However, pre/postprocess
+            %% WILL run (and we want it to) for transitivity purposes.
+            %%
+            %% Also, if skip_deps=comma,separated,app,list, then only the given
+            %% dependencies are skipped.
+            NewConfig = case rebar_config:get_global(Config3, skip_deps, false) of
+                "true" ->
+                    lists:foldl(
+                        fun(#dep{dir = Dir}, C) ->
+                                rebar_config:set_skip_dir(C, Dir)
+                        end, Config3, AvailableDeps);
+                Apps when is_list(Apps) ->
+                    SkipApps = [list_to_atom(App) || App <- string:tokens(Apps, ",")],
+                    lists:foldl(
+                        fun(#dep{dir = Dir, app = App}, C) ->
+                                case lists:member(App, SkipApps) of
+                                    true -> rebar_config:set_skip_dir(C, Dir);
+                                    false -> C
+                                end
+                        end, Config3, AvailableDeps);
+                _ ->
+                    Config3
+            end,
+
             %% Return all the available dep directories for process
             {ok, NewConfig, dep_dirs(NonRawAvailableDeps)}
     end.