diff --git a/lib/ex_doc.ex b/lib/ex_doc.ex
index 0f62a351c..c108c3560 100644
--- a/lib/ex_doc.ex
+++ b/lib/ex_doc.ex
@@ -22,7 +22,7 @@ defmodule ExDoc do
     end
 
     {module_nodes, filtered_nodes} = config.retriever.docs_from_dir(config.source_beam, config)
-    find_formatter(config.formatter).run({module_nodes, filtered_nodes}, config)
+    find_formatter(config.formatter).run(module_nodes, filtered_nodes, config)
   end
 
   # Short path for programmatic interface
diff --git a/lib/ex_doc/formatter/epub.ex b/lib/ex_doc/formatter/epub.ex
index 800bbfc3b..2db45ba35 100644
--- a/lib/ex_doc/formatter/epub.ex
+++ b/lib/ex_doc/formatter/epub.ex
@@ -8,12 +8,8 @@ defmodule ExDoc.Formatter.EPUB do
   @doc """
   Generate EPUB documentation for the given modules.
   """
-  @spec run(list, ExDoc.Config.t()) :: String.t()
-  def run(project_nodes, config) when is_list(project_nodes) and is_map(config) do
-    run({project_nodes, []}, config)
-  end
-
-  def run({project_nodes, filtered_modules}, config) when is_map(config) do
+  @spec run([ExDoc.ModuleNode.t()], [ExDoc.ModuleNode.t()], ExDoc.Config.t()) :: String.t()
+  def run(project_nodes, filtered_modules, config) when is_map(config) do
     parent = config.output
     config = normalize_config(config)
 
diff --git a/lib/ex_doc/formatter/html.ex b/lib/ex_doc/formatter/html.ex
index 723fee3f6..75f7c323b 100644
--- a/lib/ex_doc/formatter/html.ex
+++ b/lib/ex_doc/formatter/html.ex
@@ -10,17 +10,8 @@ defmodule ExDoc.Formatter.HTML do
   @doc """
   Generate HTML documentation for the given modules.
   """
-  @spec run(
-          [ExDoc.ModuleNode.t()]
-          | {[ExDoc.ModuleNode.t()], [ExDoc.ModuleNode.t()]},
-          ExDoc.Config.t()
-        ) :: String.t()
-
-  def run(project_nodes, config) when is_list(project_nodes) and is_map(config) do
-    run({project_nodes, []}, config)
-  end
-
-  def run({project_nodes, filtered_modules}, config) when is_map(config) do
+  @spec run([ExDoc.ModuleNode.t()], [ExDoc.ModuleNode.t()], ExDoc.Config.t()) :: String.t()
+  def run(project_nodes, filtered_modules, config) when is_map(config) do
     config = normalize_config(config)
     config = %{config | output: Path.expand(config.output)}
 
diff --git a/lib/ex_doc/retriever.ex b/lib/ex_doc/retriever.ex
index 5be588d0e..7a5bcf509 100644
--- a/lib/ex_doc/retriever.ex
+++ b/lib/ex_doc/retriever.ex
@@ -19,18 +19,25 @@ defmodule ExDoc.Retriever do
   @spec docs_from_dir(Path.t() | [Path.t()], ExDoc.Config.t()) ::
           {[ExDoc.ModuleNode.t()], [ExDoc.ModuleNode.t()]}
   def docs_from_dir(dir, config) when is_binary(dir) do
-    files = Path.wildcard(Path.expand("*.beam", dir))
-
-    files
-    |> Enum.map(&filename_to_module/1)
-    |> docs_from_modules(config)
+    dir
+    |> docs_from_dir({[], []}, config)
+    |> sort_modules(config)
   end
 
   def docs_from_dir(dirs, config) when is_list(dirs) do
-    Enum.flat_map(dirs, &docs_from_dir(&1, config))
+    dirs
+    |> Enum.reduce({[], []}, &docs_from_dir(&1, &2, config))
     |> sort_modules(config)
   end
 
+  defp docs_from_dir(dir, acc, config) do
+    files = Path.wildcard(Path.expand("*.beam", dir))
+
+    files
+    |> Enum.map(&filename_to_module/1)
+    |> docs_from_modules(acc, config)
+  end
+
   @doc """
   Extract documentation from all modules and returns a tuple containing
   `{modules, filtered}`, two lists of modules that were extracted and filtered
@@ -39,8 +46,11 @@ defmodule ExDoc.Retriever do
   @spec docs_from_modules([atom], ExDoc.Config.t()) ::
           {[ExDoc.ModuleNode.t()], [ExDoc.ModuleNode.t()]}
   def docs_from_modules(modules, config) when is_list(modules) do
-    modules
-    |> Enum.reduce({[], []}, fn module_name, {modules, filtered} = acc ->
+    modules |> docs_from_modules({[], []}, config) |> sort_modules(config)
+  end
+
+  defp docs_from_modules(modules, acc, config) do
+    Enum.reduce(modules, acc, fn module_name, {modules, filtered} = acc ->
       case get_module(module_name, config) do
         {:error, _module} ->
           acc
@@ -51,7 +61,6 @@ defmodule ExDoc.Retriever do
             else: {modules, [module_node | filtered]}
       end
     end)
-    |> sort_modules(config)
   end
 
   defp sort_modules({modules, filtered}, config) do
diff --git a/test/ex_doc/formatter/html/search_data_test.exs b/test/ex_doc/formatter/html/search_data_test.exs
index 15a4c2302..b2ee448e0 100644
--- a/test/ex_doc/formatter/html/search_data_test.exs
+++ b/test/ex_doc/formatter/html/search_data_test.exs
@@ -245,7 +245,7 @@ defmodule ExDoc.Formatter.HTML.SearchDataTest do
   defp search_data(modules, config) do
     {modules, []} = ExDoc.Retriever.docs_from_modules(modules, config)
 
-    ExDoc.Formatter.HTML.run(modules, config)
+    ExDoc.Formatter.HTML.run(modules, [], config)
     [path] = Path.wildcard(Path.join([config.output, "dist", "search_data-*.js"]))
     "searchData=" <> json = File.read!(path)
     Jason.decode!(json)
diff --git a/test/ex_doc/retriever_test.exs b/test/ex_doc/retriever_test.exs
index c2b842bd0..c138c0e07 100644
--- a/test/ex_doc/retriever_test.exs
+++ b/test/ex_doc/retriever_test.exs
@@ -206,6 +206,11 @@ defmodule ExDoc.RetrieverTest do
              [%{id: "A"}, %{id: "A.A"}],
              [%{id: "B"}]
            } = Retriever.docs_from_dir(ebin_dir, config)
+
+    assert {
+             [%{id: "A"}, %{id: "A.A"}],
+             [%{id: "B"}]
+           } = Retriever.docs_from_dir([ebin_dir], config)
   end
 
   test "natural sorting", c do
diff --git a/test/ex_doc_test.exs b/test/ex_doc_test.exs
index be412ff31..525b60f70 100644
--- a/test/ex_doc_test.exs
+++ b/test/ex_doc_test.exs
@@ -12,7 +12,7 @@ defmodule ExDocTest do
 
   # Simple formatter that returns whatever is passed into it
   defmodule IdentityFormatter do
-    def run(modules, config) do
+    def run(modules, _filtered, config) do
       {modules, config}
     end
   end
@@ -63,7 +63,7 @@ defmodule ExDocTest do
       source_beam: "beam_dir"
     ]
 
-    assert {{source_dir, _retr_config}, _config} = ExDoc.generate_docs("Elixir", "1", options)
+    assert {source_dir, _config} = ExDoc.generate_docs("Elixir", "1", options)
     assert source_dir == options[:source_beam]
   end