diff --git a/.gitignore b/.gitignore
index b9d8296..71660da 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,3 +17,4 @@ erl_crash.dump
 *.ez
 
 /.elixir_ls
+/.lexical
diff --git a/lib/ecto/soft_delete_repo.ex b/lib/ecto/soft_delete_repo.ex
index f0bc4ea..9a0e782 100644
--- a/lib/ecto/soft_delete_repo.ex
+++ b/lib/ecto/soft_delete_repo.ex
@@ -81,11 +81,37 @@ defmodule Ecto.SoftDelete.Repo do
         if has_include_deleted_at_clause?(query) || opts[:with_deleted] || !soft_deletable?(query) do
           {query, opts}
         else
-          query = from(x in query, where: is_nil(x.deleted_at))
+          query = filter_soft_deleted(query)
           {query, opts}
         end
       end
 
+      # We need to check the entire query and apply filtering
+      # where appropriate.  So, we recurse the query here and
+      # rebuild it with filtering where appropriate.  This
+      # currently only considers the source and does not handle
+      # things like joins...
+      defp filter_soft_deleted(%Ecto.Query{from: %{source: {_schema, _module}}} = query) do
+        if Ecto.SoftDelete.Query.soft_deletable?(query) do
+          from(x in query, where: is_nil(x.deleted_at))
+        else
+          query
+        end
+      end
+
+      defp filter_soft_deleted(%Ecto.SubQuery{query: query} = sub) do
+        if Ecto.SoftDelete.Query.soft_deletable?(query) do
+          %{sub | query: from(x in query, where: is_nil(x.deleted_at))}
+        else
+          sub
+        end
+      end
+
+      defp filter_soft_deleted(%Ecto.Query{from: from} = query) do
+        updated_from = %{from | source: filter_soft_deleted(from.source)}
+        %{query | from: updated_from}
+      end
+
       # Checks the query to see if it contains a where not is_nil(deleted_at)
       # if it does, we want to be sure that we don't exclude soft deleted records
       defp has_include_deleted_at_clause?(%Ecto.Query{wheres: wheres}) do
diff --git a/test/soft_delete_repo_test.exs b/test/soft_delete_repo_test.exs
index 98c6da6..d1cc1da 100644
--- a/test/soft_delete_repo_test.exs
+++ b/test/soft_delete_repo_test.exs
@@ -115,6 +115,16 @@ defmodule Ecto.SoftDelete.Repo.Test do
       assert Enum.member?(results, soft_deleted_user)
     end
 
+    test "handles subquery that does not expose deleted_at as 'main' schema" do
+      Repo.insert!(%User{email: "test0@example.com"})
+      Repo.insert!(%Nondeletable{value: "stuff"})
+
+      subq = User |> where([u], u.email == "test0@example.com") |> select([u], %{id: u.id, email: u.email})
+      query = subquery(subq) |> join(:left, [u], nondel in Nondeletable, on: u.id == nondel.id)
+
+      Repo.all(query)
+    end
+
     test "includes soft deleted records if where not is_nil(deleted_at) clause is present" do
       user = Repo.insert!(%User{email: "test0@example.com"})