diff --git a/lib/elixir/lib/module/parallel_checker.ex b/lib/elixir/lib/module/parallel_checker.ex
index 7627428d31..f3211a37ad 100644
--- a/lib/elixir/lib/module/parallel_checker.ex
+++ b/lib/elixir/lib/module/parallel_checker.ex
@@ -212,9 +212,14 @@ defmodule Module.ParallelChecker do
 
   defp collect_results(count, warnings, errors) do
     receive do
-      {:diagnostic, %{file: file} = diagnostic, read_snippet} ->
+      {:diagnostic, %{file: file, source: source} = diagnostic, read_snippet} ->
         :elixir_errors.print_diagnostic(diagnostic, read_snippet)
-        diagnostic = %{diagnostic | file: file && Path.absname(file)}
+
+        diagnostic = %{
+          diagnostic
+          | file: file && Path.absname(file),
+            source: source && Path.absname(source)
+        }
 
         if Map.get(diagnostic, :severity, :warning) == :error do
           collect_results(count, warnings, [diagnostic | errors])
diff --git a/lib/elixir/test/elixir/module/types/integration_test.exs b/lib/elixir/test/elixir/module/types/integration_test.exs
index fa1db95edd..3765f0e480 100644
--- a/lib/elixir/test/elixir/module/types/integration_test.exs
+++ b/lib/elixir/test/elixir/module/types/integration_test.exs
@@ -865,10 +865,18 @@ defmodule Module.Types.IntegrationTest do
       files = %{
         "a.ex" => """
         defmodule A do
+          @after_verify __MODULE__
           @file "generated.ex"
           def fun(arg) do
             :ok = List.to_tuple(arg)
           end
+
+          def __after_verify__(__MODULE__) do
+            IO.warn("This is a manually emitted warning",
+              file: Path.relative_to_cwd(__ENV__.file),
+              line: __ENV__.line
+            )
+          end
         end
         """
       }
@@ -880,6 +888,11 @@ defmodule Module.Types.IntegrationTest do
                  message: "the following pattern will never match" <> _,
                  file: file,
                  source: source
+               },
+               %{
+                 message: "This is a manually emitted warning",
+                 file: file2,
+                 source: source2
                }
              ] = warnings.runtime_warnings
 
@@ -887,6 +900,10 @@ defmodule Module.Types.IntegrationTest do
       assert Path.type(source) == :absolute
       assert String.ends_with?(file, "generated.ex")
       assert Path.type(file) == :absolute
+      assert String.ends_with?(source2, "a.ex")
+      assert Path.type(source2) == :absolute
+      assert String.ends_with?(file2, "a.ex")
+      assert Path.type(file2) == :absolute
     after
       purge(A)
     end
diff --git a/lib/mix/test/mix/tasks/compile.elixir_test.exs b/lib/mix/test/mix/tasks/compile.elixir_test.exs
index dc1e0b1286..ca83b53be8 100644
--- a/lib/mix/test/mix/tasks/compile.elixir_test.exs
+++ b/lib/mix/test/mix/tasks/compile.elixir_test.exs
@@ -1313,6 +1313,37 @@ defmodule Mix.Tasks.Compile.ElixirTest do
     end)
   end
 
+  test "tracks warnings from after_verify with relative paths" do
+    in_fixture("no_mixfile", fn ->
+      Mix.Project.push(MixTest.Case.Sample)
+
+      File.write!("lib/a.ex", """
+      defmodule A do
+        @after_verify __MODULE__
+
+        def __after_verify__(__MODULE__) do
+          IO.warn("oops", file: Path.relative_to_cwd(__ENV__.file), line: 13)
+        end
+      end
+      """)
+
+      # after_verify runs in the checker, which must make source and file absolute
+      file = Path.absname("lib/a.ex")
+
+      assert capture_io(:stderr, fn ->
+               assert {:ok,
+                       [%Mix.Task.Compiler.Diagnostic{source: ^file, file: ^file, position: 13}]} =
+                        Mix.Tasks.Compile.Elixir.run([])
+
+               assert {:noop,
+                       [%Mix.Task.Compiler.Diagnostic{source: ^file, file: ^file, position: 13}]} =
+                        Mix.Tasks.Compile.Elixir.run(["--all-warnings"])
+             end) =~ "oops"
+
+      purge([A])
+    end)
+  end
+
   test "recompiles modules with exports tracking" do
     Process.register(self(), __MODULE__)
     Code.put_compiler_option(:tracers, [__MODULE__])