diff --git a/src/rebar3_ex_doc.erl b/src/rebar3_ex_doc.erl
index ecae5a5..93cbc43 100644
--- a/src/rebar3_ex_doc.erl
+++ b/src/rebar3_ex_doc.erl
@@ -170,7 +170,10 @@ gen_chunks(State, App) ->
 ex_doc(State, App, EdocOutDir) ->
     AppName = rebar_utils:to_list(rebar_app_info:name(App)),
     {Opts, _Args} = rebar_state:command_parsed_args(State),
-    CommandStr = make_command_string(State, App, EdocOutDir, Opts),
+    % We replace output default ( "doc" ), with undefined here to keep decision logic for which output
+    % value to use later simple (i.e., output provided on CLI or in config).
+    Opts1 = lists:map(fun ({output, "doc"}) -> {output, undefined}; (Prop) -> Prop end, Opts),
+    CommandStr = make_command_string(State, App, EdocOutDir, Opts1),
     rebar_api:info("Running ex_doc for ~ts", [AppName]),
     case rebar_utils:sh(CommandStr, [{return_on_error, true}]) of
         {ok, []} ->
@@ -204,10 +207,8 @@ make_command_string(State, App, EdocOutDir, Opts) ->
         SourceRefVer,
         "--config",
         ex_doc_config_file(App, EdocOutDir),
-        "--output",
-        output_dir(App, Opts),
         "--quiet"
-    ] ++ maybe_package_arg(PkgName, rebar_app_info:get(App, ex_doc, [])),
+    ] ++ maybe_add_output_dir(App, Opts) ++ maybe_package_arg(PkgName, rebar_app_info:get(App, ex_doc, [])),
     DepPaths = rebar_state:code_paths(State, all_deps),
     PathArgs = lists:foldl(
         fun(Path, Args) -> ["--paths", Path | Args] end,
@@ -222,6 +223,16 @@ make_command_string(State, App, EdocOutDir, Opts) ->
     ),
     string:join(CommandArgs, " ").
 
+maybe_add_output_dir(App, Opts) ->
+    case {proplists:get_value(output, Opts, undefined), get_exdoc_opt(App, output)} of
+        {undefined, undefined} ->
+            ["--output", output_dir(App, ?DEFAULT_DOC_DIR)];
+        {OutputDir, _} when OutputDir =/= undefined ->
+            ["--output", output_dir(App, OutputDir)];
+        {undefined, Specified}  ->
+            ["--output", output_dir(App, Specified)]
+    end.
+
 maybe_package_arg(PkgName, Opts) when Opts =:= []
                                       orelse is_tuple(hd(Opts))
                                       orelse is_atom(hd(Opts)) ->
@@ -270,15 +281,30 @@ win32_ex_doc_script(Path) ->
 
 -spec ex_doc_config_file(rebar_app_info:t(), file:filename()) -> file:filename().
 ex_doc_config_file(App, EdocOutDir) ->
+    case  get_exdoc_opts(App) of
+        {config_file, FilePath} ->
+            FilePath;
+        Opts ->
+            ExDocOpts = to_ex_doc_format(Opts),
+            ExDocConfigFile = filename:join([EdocOutDir, "docs.config"]),
+            ok = write_config(ExDocConfigFile, ExDocOpts),
+            ExDocConfigFile
+    end.
+
+get_exdoc_opts(App) ->
     case rebar_app_info:get(App, ex_doc, []) of
         ExDocOpts0 when ExDocOpts0 =:= [] orelse is_tuple(hd(ExDocOpts0)) orelse is_atom(hd(ExDocOpts0)) ->
-            ExDocOpts1 = ex_doc_opts_defaults(ExDocOpts0),
-            ExDocOpts2 = to_ex_doc_format(ExDocOpts1),
-            ExDocConfigFile = filename:join([EdocOutDir, "docs.config"]),
-            ok = write_config(ExDocConfigFile, ExDocOpts2),
-            ExDocConfigFile;
+            ex_doc_opts_defaults(ExDocOpts0);
         ExDocConfigFile ->
-            ExDocConfigFile
+            {config_file, ExDocConfigFile}
+    end.
+
+get_exdoc_opt(App, OptName) ->
+    case get_exdoc_opts(App) of
+        {config_file, _} ->
+            undefined;
+        Opts ->
+            proplists:get_value(OptName, Opts, undefined)
     end.
 
 to_ex_doc_format(ExDocOpts) ->
@@ -400,9 +426,8 @@ maybe_add_opt(logo, Opts) ->
             ["--logo", Logo]
     end.
 
--spec output_dir(rebar_app_info:t(), proplists:proplist()) -> file:filename().
-output_dir(App, Opts) ->
-    Dir = proplists:get_value(output, Opts, ?DEFAULT_DOC_DIR),
+-spec output_dir(any(), file:filename()) -> file:filename().
+output_dir(App, Dir) ->
     filename:join(rebar_app_info:dir(App), Dir).
 
 -spec write_config(file:filename(), proplists:proplist()) -> ok.
diff --git a/test/rebar3_ex_doc_SUITE.erl b/test/rebar3_ex_doc_SUITE.erl
index ac68ed3..369ca1f 100644
--- a/test/rebar3_ex_doc_SUITE.erl
+++ b/test/rebar3_ex_doc_SUITE.erl
@@ -11,6 +11,8 @@ all() ->
         generate_docs_with_current_app_set,
         generate_docs_with_bad_config,
         generate_docs_with_alternate_ex_doc,
+        generate_docs_with_output_set_in_config,
+        generate_docs_overriding_output_set_in_config,
         format_errors
     ].
 
@@ -43,7 +45,7 @@ generate_docs(Config) ->
     ok = make_readme(App),
     ok = make_license(App),
     {ok, _} = rebar3_ex_doc:do(State),
-    check_docs(App, StubConfig).
+    check_docs(App, State, StubConfig).
 
 generate_docs_alternate_rebar3_config_format(Config) ->
     StubConfig = #{
@@ -67,7 +69,7 @@ generate_docs_alternate_rebar3_config_format(Config) ->
     ok = make_readme(App),
     ok = make_license(App),
     {ok, _} = rebar3_ex_doc:do(State),
-    check_docs(App, StubConfig).
+    check_docs(App, State, StubConfig).
 
 generate_docs_with_alternate_ex_doc(Config) ->
     Priv = code:priv_dir(rebar3_ex_doc),
@@ -93,7 +95,7 @@ generate_docs_with_alternate_ex_doc(Config) ->
     ok = make_readme(App),
     ok = make_license(App),
     {ok, _} = rebar3_ex_doc:do(State),
-    check_docs(App, StubConfig),
+    check_docs(App, State, StubConfig),
 
     StubConfig1 = #{
         app_src => #{version => "0.1.0"},
@@ -130,7 +132,7 @@ generate_docs_with_current_app_set(Config) ->
     ok = make_readme(App),
     ok = make_license(App),
     {ok, _} = rebar3_ex_doc:do(State1),
-    check_docs(App, StubConfig).
+    check_docs(App, State, StubConfig).
 
 generate_docs_with_bad_config(Config) ->
     StubConfig = #{
@@ -149,6 +151,47 @@ generate_docs_with_bad_config(Config) ->
     ok = make_license(App),
     ?assertError({error, {rebar3_ex_doc, {ex_doc, _}}}, rebar3_ex_doc:do(State)).
 
+generate_docs_with_output_set_in_config(Config) ->
+    StubConfig = #{
+        app_src => #{version => "0.1.0"},
+        dir => data_dir(Config),
+        name => "output_set_in_config_docs",
+        config =>
+            {ex_doc, [
+                {source_url, <<"https://github.com/eh/eh">>},
+                {extras, [<<"README.md">>, <<"LICENSE">>]},
+                {main, <<"readme">>},
+                {output, "foo_docs"}
+            ]}
+    },
+    {State, App} = make_stub(StubConfig),
+
+    ok = make_readme(App),
+    ok = make_license(App),
+    {ok, _} = rebar3_ex_doc:do(State),
+    check_docs(App, State, StubConfig).
+
+generate_docs_overriding_output_set_in_config(Config) ->
+    StubConfig = #{
+        app_src => #{version => "0.1.0"},
+        dir => data_dir(Config),
+        args => "--output bar_docs",
+        name => "override_output_set_in_config_docs",
+        config =>
+            {ex_doc, [
+                {source_url, <<"https://github.com/eh/eh">>},
+                {extras, [<<"README.md">>, <<"LICENSE">>]},
+                {main, <<"readme">>},
+                {output, "foo_docs"}
+            ]}
+    },
+    {State, App} = make_stub(StubConfig),
+
+    ok = make_readme(App),
+    ok = make_license(App),
+    {ok, _} = rebar3_ex_doc:do(State),
+    check_docs(App, State, StubConfig).
+
 format_errors(_) ->
     Err = "The app 'foo' specified was not found.",
     ?assertEqual(Err, rebar3_ex_doc:format_error({app_not_found, foo})),
@@ -170,16 +213,17 @@ format_errors(_) ->
     Err5 = "An unknown error has occurred. Run with DIAGNOSTICS=1 for more details.",
     ?assertEqual(Err5, rebar3_ex_doc:format_error({eh, some_error})).
 
-check_docs(App, #{config := {ex_doc, DocConfig}} = _Stub) ->
+check_docs(App, State, #{config := {ex_doc, DocConfig}} = _Stub) ->
     Extras = format_extras(proplists:get_value(extras, DocConfig)),
     AppDir = rebar_app_info:dir(App),
     BuildDir = filename:join(AppDir, "_build"),
     {ok, ConfigFile} = file:consult(filename:join([BuildDir, "default/lib/", rebar_app_info:name(App), "doc/docs.config"])),
-    ExpExtras = proplists:get_value(extras, ConfigFile), 
+    ExpExtras = proplists:get_value(extras, ConfigFile),
     ?assertMatch(Extras, ExpExtras),
     AppName = rebar_app_info:name(App),
     AppNameStr = rebar_utils:to_list(AppName),
-    DocDir = filename:join(AppDir, "doc"),
+    {Opts, _Args} = rebar_state:command_parsed_args(State),
+    DocDir = filename:join(AppDir, get_doc_dir(Opts, DocConfig)),
     {ok, IndexDoc} = file:read_file(filename:join(DocDir, "index.html")),
     {ok, ModuleDoc} = file:read_file(filename:join(DocDir, AppNameStr ++ ".html")),
     {ok, ReadMeDoc} = file:read_file(filename:join(DocDir, "readme.html")),
@@ -200,7 +244,15 @@ check_docs(App, #{config := {ex_doc, DocConfig}} = _Stub) ->
         re:run(EpubReadMe, "PLEASE READ ME", [{capture, [0], binary}])
     ).
 
-format_extras(Extras0) -> 
+get_doc_dir(Opts, DocConfig) ->
+    case proplists:get_value(output, Opts, proplists:get_value(output, DocConfig, "doc")) of
+        undefined ->
+            "doc";
+        Doc ->
+            Doc
+    end.
+
+format_extras(Extras0) ->
     lists:foldr(
         fun ({Extra, ExtraOpts}, Extras) ->
                 [{list_to_atom(Extra), format_extras_opts(ExtraOpts)} | Extras];
@@ -218,7 +270,7 @@ format_extras_opts(Extras) ->
         fun (filename, Filename) when is_list(Filename) ->
                 list_to_binary(Filename);
             (title, Title) when is_list(Title) ->
-                list_to_binary(Title); 
+                list_to_binary(Title);
             (_Key, Value) ->
                 Value
         end,