diff --git a/src/erlfmt_cli.erl b/src/erlfmt_cli.erl
index 8ba30f9..bea1e6c 100644
--- a/src/erlfmt_cli.erl
+++ b/src/erlfmt_cli.erl
@@ -107,8 +107,26 @@ with_parsed(Name, Config) ->
             erlang:halt(127)
     end.
 
+-spec set_difference([file:name_all()], [file:name_all()]) -> [file:name_all()].
 set_difference(Files, Excludes) ->
-    sets:to_list(sets:subtract(sets:from_list(Files), sets:from_list(Excludes))).
+    {ok, Cwd} = file:get_cwd(),
+    AbsoluteFiles = maps:from_list([{resolve_path(Cwd, F), F} || F <- Files]),
+    AbsoluteExcludes = [resolve_path(Cwd, E) || E <- Excludes],
+    maps:values(maps:without(AbsoluteExcludes, AbsoluteFiles)).
+
+resolve_path(Dir, Filename) ->
+    resolve_path2(filename:absname(Filename, Dir)).
+
+resolve_path2(AbsPath) ->
+    [Volume | Components] = filename:split(AbsPath),
+    filename:join(resolve_path2(Components, [Volume])).
+
+resolve_path2([".." | T1], [Volume]) -> resolve_path2(T1, [Volume]);
+resolve_path2([<<"..">> | T1], [Volume]) -> resolve_path2(T1, [Volume]);
+resolve_path2([".." | T1], [_H2 | T2]) -> resolve_path2(T1, T2);
+resolve_path2([<<"..">> | T1], [_H2 | T2]) -> resolve_path2(T1, T2);
+resolve_path2([H1 | T1], Components) -> resolve_path2(T1, [H1 | Components]);
+resolve_path2([], Components) -> lists:reverse(Components).
 
 %% needed because of getopt
 -dialyzer({nowarn_function, [unprotected_with_config/2]}).
diff --git a/test/erlfmt_cli_SUITE.erl b/test/erlfmt_cli_SUITE.erl
index 8afcdc1..6866f18 100644
--- a/test/erlfmt_cli_SUITE.erl
+++ b/test/erlfmt_cli_SUITE.erl
@@ -51,6 +51,7 @@
     noformat_pragma/1,
     noformat_pragma_file/1,
     exclude_check/1,
+    exclude_absolute_check/1,
     range_check_full/1,
     range_check_partial/1
 ]).
@@ -98,6 +99,7 @@ groups() ->
             noformat_pragma,
             noformat_pragma_file,
             exclude_check,
+            exclude_absolute_check,
             range_check_full,
             range_check_partial
         ]}
@@ -250,16 +252,14 @@ noformat_pragma(Config) when is_list(Config) ->
 exclude_check(Config) when is_list(Config) ->
     Files = filename:join(?config(data_dir, Config), "*.erl"),
     Exclude = filename:join(?config(data_dir, Config), "broken.erl"),
-    WithBroken = os:cmd(
-        escript() ++ " -c " ++ Files
-    ),
-    ?assertNotMatch(nomatch, string:find(WithBroken, "[warn]")),
-    ?assertNotMatch(nomatch, string:find(WithBroken, "broken.erl")),
-    WithoutBroken = os:cmd(
-        escript() ++ " -c " ++ Files ++ " --exclude-files=" ++ Exclude
-    ),
-    ?assertNotMatch(nomatch, string:find(WithoutBroken, "[warn]")),
-    ?assertMatch(nomatch, string:find(WithoutBroken, "broken.erl")).
+    exclude_test(Files, Exclude).
+
+exclude_absolute_check(Config) when is_list(Config) ->
+    {ok, ProjectRoot} = file:get_cwd(),
+    DataDirRelPath = make_relative_path(?config(data_dir, Config), ProjectRoot),
+    Files = filename:join(?config(data_dir, Config), "*.erl"),
+    Exclude = filename:join(DataDirRelPath, "broken.erl"),
+    exclude_test(Files, Exclude).
 
 range_check_full(Config) when is_list(Config) ->
     %% Mainly check the options is properly recognized.
@@ -284,6 +284,27 @@ stdio_test(FileName, Options, Config) ->
     {ok, Expected} = file:read_file(Path),
     assert_diagnostic:assert_binary_match(Expected, unicode:characters_to_binary(Formatted)).
 
+exclude_test(Files, Exclude) ->
+    WithBroken = os:cmd(
+        escript() ++ " -c " ++ Files
+    ),
+    ?assertNotMatch(nomatch, string:find(WithBroken, "[warn]")),
+    ?assertNotMatch(nomatch, string:find(WithBroken, "broken.erl")),
+    WithoutBroken = os:cmd(
+        escript() ++ " -c " ++ Files ++ " --exclude-files=" ++ Exclude
+    ),
+    ?assertNotMatch(nomatch, string:find(WithoutBroken, "[warn]")),
+    ?assertMatch(nomatch, string:find(WithoutBroken, "broken.erl")).
+
 escript() ->
     %% this relies on the _build structure rebar3 uses
     filename:join(code:lib_dir(erlfmt), "../../bin/erlfmt").
+
+make_relative_path(Source, Target) ->
+    make_relative_path2(filename:split(Source), filename:split(Target)).
+
+make_relative_path2([H | T1], [H | T2]) ->
+    make_relative_path2(T1, T2);
+make_relative_path2(Source, Target) ->
+    Base = lists:duplicate(length(Target), ".."),
+    filename:join(Base ++ Source).