diff --git a/src/rebar_opts.erl b/src/rebar_opts.erl
index 8195a775..8b157e60 100644
--- a/src/rebar_opts.erl
+++ b/src/rebar_opts.erl
@@ -151,10 +151,10 @@ add_opt(Opts1, Opts2) ->
 del_opt(Opts1, Opts2) ->
     lists:foldl(fun({deps, Value}, OptsAcc) ->
                         OldValue = ?MODULE:get(OptsAcc, {deps,default}, []),
-                        set(OptsAcc, {deps,default}, OldValue--Value);
+                        set(OptsAcc, {deps,default}, del_dep(OldValue, Value));
                    ({Key, Value}, OptsAcc) ->
                         OldValue = ?MODULE:get(OptsAcc, Key, []),
-                        set(OptsAcc, Key, OldValue--Value)
+                        set(OptsAcc, Key, del_dep(OldValue, Value))
                 end, Opts2, Opts1).
 
 override_opt(Opts1, Opts2) ->
@@ -164,6 +164,25 @@ override_opt(Opts1, Opts2) ->
                         set(OptsAcc, Key, Value)
                 end, Opts2, Opts1).
 
+%% @private
+del_dep(OldValue, [Value]) when is_atom(Value) ->
+    NewValue = lists:keydelete(atom_to_binary(Value, utf8), 1, OldValue),
+    del_dep(NewValue, OldValue, [Value]);
+del_dep(OldValue, [{Value, _Version, _Source}]) ->
+    NewValue = lists:keydelete(atom_to_binary(Value, utf8), 1, OldValue),
+    del_dep(NewValue, OldValue, [{Value, _Version, _Source}]);
+del_dep(OldValue, [Value|Values]) ->
+    NewValue = del_dep(del_dep(OldValue, [Value]), OldValue, [Value]),
+    del_dep(NewValue, Values).
+
+%% @private
+%% If the initial deletion did not work remove it as always
+%% to ensure rebar3 at least maintains its old behaviour.
+del_dep(OldValue, OldValue, Value) ->
+    OldValue--Value;
+del_dep(NewValue, _OldValue, _Value) ->
+    NewValue.
+
 %%
 %% Function for dict:merge/3 (in merge_opts/2) to merge options by priority.
 %%
diff --git a/test/rebar_compile_SUITE.erl b/test/rebar_compile_SUITE.erl
index ed05bf48..36ee8b2f 100644
--- a/test/rebar_compile_SUITE.erl
+++ b/test/rebar_compile_SUITE.erl
@@ -28,7 +28,7 @@ all() ->
      umbrella_mib_first_test, only_default_transitive_deps, clean_all,
      clean_specific, profile_deps, deps_build_in_prod, only_deps,
      override_deps, git_subdir_deps, override_add_deps, override_del_deps,
-     override_opts, override_add_opts, override_del_opts,
+     override_del_pkg_deps, override_opts, override_add_opts, override_del_opts,
      apply_overrides_exactly_once, override_only_deps,
      profile_override_deps, profile_override_add_deps, profile_override_del_deps,
      profile_override_opts, profile_override_add_opts, profile_override_del_opts,
@@ -1608,6 +1608,28 @@ override_del_deps(Config) ->
               {dep, "dep_d"}]}
     ).
 
+override_del_pkg_deps(Config) ->
+    Deps = rebar_test_utils:expand_deps(pkg, [{"some_dep", "0.0.1", [{"other_dep", "0.0.1", []}]}]),
+    TopDeps = rebar_test_utils:top_level_deps(Deps),
+
+    {_, PkgDeps} = rebar_test_utils:flat_deps(Deps),
+    mock_pkg_resource:mock([{pkgdeps, PkgDeps}]),
+
+    RebarConfig = [
+        {deps, TopDeps},
+        {overrides, [
+            {del, some_dep, [
+                {deps, [other_dep]}
+            ]}
+        ]}
+    ],
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{dep, "some_dep"},
+              {dep_not_exist, "other_dep"}]}
+    ).
+
 override_opts(Config) ->
     AppsDir = ?config(apps, Config),