diff --git a/lib/credo/check.ex b/lib/credo/check.ex
index 15b7fc15d..91f2b7299 100644
--- a/lib/credo/check.ex
+++ b/lib/credo/check.ex
@@ -895,6 +895,38 @@ defmodule Credo.Check do
     @__default_enabled_checks__
   end
 
+  @doc false
+  def all_loaded_checks do
+    # Source credo's own checks from the curated `standard_checks/0` list
+    # rather than `:code.all_loaded/0` — until something references an
+    # unused check module the BEAM hasn't loaded it, so the all-loaded set
+    # silently misses checks that nothing has yet pulled in. That's the
+    # root of `MissingCheckInConfig` failing to flag unused checks (#1278).
+    #
+    # We supplement with check modules from any *other* loaded application
+    # (plugins, custom check libraries) by reading their module list from
+    # `:application.get_key/2`, which doesn't depend on prior code loading.
+    Enum.uniq(standard_checks() ++ external_check_modules())
+  end
+
+  defp external_check_modules do
+    for {app, _, _} <- Application.loaded_applications(),
+        app != :credo,
+        {:ok, modules} <- [:application.get_key(app, :modules)],
+        module <- modules,
+        Code.ensure_loaded?(module),
+        implements_credo_check?(module),
+        do: module
+  end
+
+  defp implements_credo_check?(module) do
+    function_exported?(module, :module_info, 1) and
+      module.module_info(:attributes)
+      |> Keyword.get_values(:behaviour)
+      |> List.flatten()
+      |> Enum.member?(__MODULE__)
+  end
+
   @doc false
   # TODO: decide whether this should live here or in `Credo.Execution`.
   def mentioned_checks(exec) do
diff --git a/test/credo/check_all_loaded_checks_test.exs b/test/credo/check_all_loaded_checks_test.exs
new file mode 100644
index 000000000..f47b6fdcd
--- /dev/null
+++ b/test/credo/check_all_loaded_checks_test.exs
@@ -0,0 +1,25 @@
+defmodule Credo.Check.AllLoadedChecksTest do
+  use ExUnit.Case, async: true
+
+  # `all_loaded_checks/0` used to source its result from `:code.all_loaded/0`,
+  # so any check module nothing had yet referenced was silently missing —
+  # which is exactly what made `MissingCheckInConfig` fail to flag unused
+  # checks (#1278). The fix sources credo's own checks from the curated
+  # `standard_checks/0` list and supplements with check modules discovered
+  # via `:application.get_key/2` on every other loaded application, so the
+  # result is independent of which modules happen to be loaded.
+
+  test "returns every standard credo check regardless of load order" do
+    all = Credo.Check.all_loaded_checks()
+    missing = Credo.Check.standard_checks() -- all
+
+    assert missing == [],
+           "expected all standard checks to be included in `all_loaded_checks/0`, " <>
+             "but these were missing: #{inspect(missing)}"
+  end
+
+  test "result contains no duplicates" do
+    all = Credo.Check.all_loaded_checks()
+    assert all == Enum.uniq(all)
+  end
+end