diff --git a/tpl/tplimpl/templatestore.go b/tpl/tplimpl/templatestore.go
index 53880eb33..c6a6d4cd5 100644
--- a/tpl/tplimpl/templatestore.go
+++ b/tpl/tplimpl/templatestore.go
@@ -1133,12 +1133,21 @@ func (s *TemplateStore) insertTemplate2(
 		tree.Insert(key, m)
 	}
 
-	if !replace {
-		if v, found := m[nk]; found {
-			if len(pi.Identifiers()) >= len(v.PathInfo.Identifiers()) {
-				// e.g. /pages/home.foo.html and  /pages/home.html where foo may be a valid language name in another site.
-				return nil, nil
-			}
+	nkExisting, existingFound := m[nk]
+	if !replace && existingFound && fi != nil && nkExisting.Fi != nil {
+		// See issue #13715.
+		// We do the merge on the file system level, but from Hugo v0.146.0 we have a situation where
+		// the project may well have a different layouts layout compared to the theme(s) it uses.
+		// We could possibly have fixed that on a lower (file system) level, but since this is just
+		// a temporary situation (until all projects are updated),
+		// do a replace here if the file comes from higher up in the module chain.
+		replace = fi.Meta().ModuleOrdinal < nkExisting.Fi.Meta().ModuleOrdinal
+	}
+
+	if !replace && existingFound {
+		if len(pi.Identifiers()) >= len(nkExisting.PathInfo.Identifiers()) {
+			// e.g. /pages/home.foo.html and  /pages/home.html where foo may be a valid language name in another site.
+			return nil, nil
 		}
 	}
 
diff --git a/tpl/tplimpl/templatestore_integration_test.go b/tpl/tplimpl/templatestore_integration_test.go
index 75ec0376f..e10d7149a 100644
--- a/tpl/tplimpl/templatestore_integration_test.go
+++ b/tpl/tplimpl/templatestore_integration_test.go
@@ -1103,6 +1103,23 @@ All.
 	b.AssertLogContains("unrecognized render hook")
 }
 
+func TestLayoutOverrideThemeWhenThemeOnOldFormatIssue13715(t *testing.T) {
+	t.Parallel()
+
+	files := `
+-- hugo.toml --
+theme = "mytheme"
+-- layouts/list.html --
+ layouts/list.html
+-- themes/mytheme/layouts/_default/list.html --
+mytheme/layouts/_default/list.html
+
+`
+
+	b := hugolib.Test(t, files)
+	b.AssertFileContent("public/index.html", "layouts/list.html")
+}
+
 func BenchmarkExecuteWithContext(b *testing.B) {
 	files := `
 -- hugo.toml --