diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5453669066..eaa3836d07 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog for v3.x
 
+## Unreleased
+
+### Enhancements
+
+  * [Ecto.Repo] Preload custom queries with `order_by` now take precedence over `:preload_order`. The `:preload_order` option is now only applied when no custom query with ordering is provided.
+
 ## v3.13.3 (2025-09-19)
 
 ### Enhancements
diff --git a/integration_test/cases/preload.exs b/integration_test/cases/preload.exs
index 9e82559ccc..958f43342a 100644
--- a/integration_test/cases/preload.exs
+++ b/integration_test/cases/preload.exs
@@ -695,6 +695,23 @@ defmodule Ecto.Integration.PreloadTest do
     assert [%{name: "foz"}, %{name: "baz"}] = post2.ordered_users_by_join_table
   end
 
+  test "custom query order_by overrides preload_order" do
+    post = TestRepo.insert!(%Post{title: "1"})
+
+    TestRepo.insert!(%Comment{text: "2", post_id: post.id})
+    TestRepo.insert!(%Comment{text: "1", post_id: post.id})
+    TestRepo.insert!(%Comment{text: "3", post_id: post.id})
+
+    # Without custom query, preload_order (asc by text) should apply
+    post = TestRepo.preload(post, :ordered_comments)
+    assert [%{text: "1"}, %{text: "2"}, %{text: "3"}] = post.ordered_comments
+
+    # With custom query having order_by, it should override preload_order
+    query = from(c in Comment, order_by: [desc: c.text])
+    post = TestRepo.preload(post, [ordered_comments: query], force: true)
+    assert [%{text: "3"}, %{text: "2"}, %{text: "1"}] = post.ordered_comments
+  end
+
   ## Others
 
   @tag :invalid_prefix
diff --git a/lib/ecto/repo/preloader.ex b/lib/ecto/repo/preloader.ex
index ad7f1f7fed..a714c1b931 100644
--- a/lib/ecto/repo/preloader.ex
+++ b/lib/ecto/repo/preloader.ex
@@ -483,6 +483,11 @@ defmodule Ecto.Repo.Preloader do
 
   defp add_preload_order([], query), do: query
 
+  defp add_preload_order(_order, %{order_bys: [_|_]} = query) do
+    # Skip applying preload_order when query already has custom order_by clauses
+    query
+  end
+
   defp add_preload_order(order, query) when is_list(order) do
     Ecto.Query.prepend_order_by(query, [q], ^order)
   end
diff --git a/lib/ecto/schema.ex b/lib/ecto/schema.ex
index d54072c4ef..13a8a03929 100644
--- a/lib/ecto/schema.ex
+++ b/lib/ecto/schema.ex
@@ -786,6 +786,8 @@ defmodule Ecto.Schema do
       For example, if you set `Post.has_many :comments, preload_order: [asc: :content]`,
       whenever the `:comments` associations is preloaded,
       the comments will be ordered by the `:content` field.
+      Note that if you provide a custom query with its own `order_by` clause,
+      the custom ordering will take precedence and the `:preload_order` will not be applied.
       See `Ecto.Query.order_by/3` to learn more about ordering expressions.
 
   ## Examples
@@ -1352,6 +1354,8 @@ defmodule Ecto.Schema do
       It may be a keyword list/list of fields or an MFA tuple, such as `{Mod, fun, []}`.
       Both cases must resolve to a valid `order_by` expression. See `Ecto.Query.order_by/3`
       to learn more about ordering expressions.
+      Note that if you provide a custom query with its own `order_by` clause,
+      the custom ordering will take precedence and the `:preload_order` will not be applied.
       See the [preload order](#many_to_many/3-preload-order) section below to learn how
       this option can be utilized