diff --git a/lib/private/write_source_file.bzl b/lib/private/write_source_file.bzl
index 2789e03..ba5d592 100644
--- a/lib/private/write_source_file.bzl
+++ b/lib/private/write_source_file.bzl
@@ -372,4 +372,11 @@ def _is_file_missing(label):
     file_abs = "%s/%s" % (label.package, label.name)
     file_rel = file_abs[len(native.package_name()) + 1:]
     file_glob = native.glob([file_rel], exclude_directories = 0, allow_empty = True)
-    return len(file_glob) == 0
+
+    # Check for subpackages in case the expected output contains BUILD files,
+    # the above files glob will return empty.
+    subpackage_glob = []
+    if hasattr(native, "subpackages"):
+        subpackage_glob = native.subpackages(include = [file_rel], allow_empty = True)
+
+    return len(file_glob) == 0 and len(subpackage_glob) == 0
diff --git a/lib/tests/write_source_files/build_files_in_outs/BUILD.bazel b/lib/tests/write_source_files/build_files_in_outs/BUILD.bazel
new file mode 100644
index 0000000..337c696
--- /dev/null
+++ b/lib/tests/write_source_files/build_files_in_outs/BUILD.bazel
@@ -0,0 +1,33 @@
+load("//lib:write_source_files.bzl", "write_source_file")
+load("//lib:copy_to_directory.bzl", "copy_to_directory")
+load("@bazel_skylib//rules:write_file.bzl", "write_file")
+
+write_file(
+    name = "write_build",
+    out = "BUILD",
+    content = [
+        "# Marker for a package",
+        "",
+    ],
+)
+
+write_file(
+    name = "write_other",
+    out = "other.txt",
+    content = ["Another file"],
+)
+
+copy_to_directory(
+    name = "dir",
+    srcs = [
+        ":BUILD",
+        ":other.txt",
+    ],
+)
+
+# This will cause an analysis failure if "expected_out" is considered missing.
+write_source_file(
+    name = "build_files_in_outs",
+    in_file = ":dir",
+    out_file = ":expected_out",
+)
diff --git a/lib/tests/write_source_files/build_files_in_outs/expected_out/BUILD b/lib/tests/write_source_files/build_files_in_outs/expected_out/BUILD
new file mode 100644
index 0000000..b9c641d
--- /dev/null
+++ b/lib/tests/write_source_files/build_files_in_outs/expected_out/BUILD
@@ -0,0 +1 @@
+# Marker for a package
diff --git a/lib/tests/write_source_files/build_files_in_outs/expected_out/other.txt b/lib/tests/write_source_files/build_files_in_outs/expected_out/other.txt
new file mode 100644
index 0000000..a571642
--- /dev/null
+++ b/lib/tests/write_source_files/build_files_in_outs/expected_out/other.txt
@@ -0,0 +1 @@
+Another file
\ No newline at end of file