diff --git a/check/checktest/checktest.go b/check/checktest/checktest.go
index f2f4350..6d0e641 100644
--- a/check/checktest/checktest.go
+++ b/check/checktest/checktest.go
@@ -336,10 +336,13 @@ func compile(
 	moduleName descriptor.ModuleName,
 ) ([]descriptor.FileDescriptor, error) {
 	dirPaths = fromSlashPaths(dirPaths)
-	filePaths = fromSlashPaths(filePaths)
+	// The compiler names each file by the path it is given, and .proto file
+	// names use forward slashes even on Windows.
+	toSlashFilePaths := make([]string, len(filePaths))
 	toSlashFilePathMap := make(map[string]struct{}, len(filePaths))
-	for _, filePath := range filePaths {
-		toSlashFilePathMap[filepath.ToSlash(filePath)] = struct{}{}
+	for i, filePath := range fromSlashPaths(filePaths) {
+		toSlashFilePaths[i] = filepath.ToSlash(filePath)
+		toSlashFilePathMap[toSlashFilePaths[i]] = struct{}{}
 	}
 
 	var warningErrorsWithPos []reporter.ErrorWithPos
@@ -360,7 +363,7 @@ func compile(
 		// This is what buf uses.
 		SourceInfoMode: protocompile.SourceInfoExtraOptionLocations,
 	}
-	files, err := compiler.Compile(ctx, filePaths...)
+	files, err := compiler.Compile(ctx, toSlashFilePaths...)
 	if err != nil {
 		return nil, err
 	}
diff --git a/check/internal/example/cmd/buf-plugin-syntax-specified/main_test.go b/check/internal/example/cmd/buf-plugin-syntax-specified/main_test.go
index 77f7f85..742a7d4 100644
--- a/check/internal/example/cmd/buf-plugin-syntax-specified/main_test.go
+++ b/check/internal/example/cmd/buf-plugin-syntax-specified/main_test.go
@@ -60,3 +60,25 @@ func TestSimpleFailure(t *testing.T) {
 		},
 	}.Run(t)
 }
+
+func TestSubdirectoryFailure(t *testing.T) {
+	t.Parallel()
+
+	checktest.CheckTest{
+		Request: &checktest.RequestSpec{
+			Files: &checktest.ProtoFileSpec{
+				DirPaths:  []string{"testdata/subdirectory_failure"},
+				FilePaths: []string{"sub/simple.proto"},
+			},
+		},
+		Spec: spec,
+		ExpectedAnnotations: []checktest.ExpectedAnnotation{
+			{
+				RuleID: syntaxSpecifiedRuleID,
+				FileLocation: &checktest.ExpectedFileLocation{
+					FileName: "sub/simple.proto",
+				},
+			},
+		},
+	}.Run(t)
+}
diff --git a/check/internal/example/cmd/buf-plugin-syntax-specified/testdata/subdirectory_failure/sub/simple.proto b/check/internal/example/cmd/buf-plugin-syntax-specified/testdata/subdirectory_failure/sub/simple.proto
new file mode 100644
index 0000000..322a627
--- /dev/null
+++ b/check/internal/example/cmd/buf-plugin-syntax-specified/testdata/subdirectory_failure/sub/simple.proto
@@ -0,0 +1 @@
+package simple;