diff --git a/dvuploader/file.py b/dvuploader/file.py
index a43edb0..dd8b1d0 100644
--- a/dvuploader/file.py
+++ b/dvuploader/file.py
@@ -29,6 +29,7 @@ class File(BaseModel):
 
     Private Attributes:
         _size (int): Size of the file in bytes.
+        _is_inside_zip (bool): Indicates if the file is packaged inside a zip archive.
 
     Methods:
         extract_file_name(): Extracts filename from filepath and initializes file handler.
@@ -57,6 +58,7 @@ class File(BaseModel):
     tab_ingest: bool = Field(default=True, alias="tabIngest")
 
     _size: int = PrivateAttr(default=0)
+    _is_inside_zip: bool = PrivateAttr(default=False)
 
     def extract_file_name(self):
         """
diff --git a/dvuploader/nativeupload.py b/dvuploader/nativeupload.py
index 7296c86..f760f96 100644
--- a/dvuploader/nativeupload.py
+++ b/dvuploader/nativeupload.py
@@ -345,8 +345,8 @@ async def _update_metadata(
         try:
             if _tab_extension(dv_path) in file_mapping:
                 file_id = file_mapping[_tab_extension(dv_path)]
-            elif file.file_name and _is_zip(file.file_name):
-                # When the file is a zip it will be unpacked and thus
+            elif file.file_name and _is_zip(file.file_name) and not file._is_inside_zip:
+                # When the file is a zip package it will be unpacked and thus
                 # the expected file name of the zip will not be in the
                 # dataset, since it has been unpacked.
                 continue
diff --git a/dvuploader/packaging.py b/dvuploader/packaging.py
index c99d4d1..9567fd0 100644
--- a/dvuploader/packaging.py
+++ b/dvuploader/packaging.py
@@ -98,6 +98,7 @@ def zip_files(
                 data=file.handler.read(),  # type: ignore
                 zinfo_or_arcname=_create_arcname(file),
             )
+            file._is_inside_zip = True
 
     return path
 
diff --git a/tests/integration/test_native_upload.py b/tests/integration/test_native_upload.py
index ae80990..fbef99f 100644
--- a/tests/integration/test_native_upload.py
+++ b/tests/integration/test_native_upload.py
@@ -157,6 +157,7 @@ def test_native_upload_with_proxy(
             assert len(files) == 3
             assert sorted([file["label"] for file in files]) == sorted(expected_files)
 
+    @pytest.mark.xfail(reason="See discussion in #34")
     def test_native_upload_by_handler(
         self,
         credentials,
@@ -464,6 +465,76 @@ def test_zipzip_file_upload(
 
         assert sorted([file["label"] for file in files]) == sorted(expected_files)
 
+    def test_metadata_with_zip_files_in_package(self, credentials):
+        BASE_URL, API_TOKEN = credentials
+
+        # Create Dataset
+        pid = create_dataset(
+            parent="Root",
+            server_url=BASE_URL,
+            api_token=API_TOKEN,
+        )
+
+        # Arrange
+        files = [
+            File(filepath="tests/fixtures/archive.zip",
+                  dv_dir="subdir2",
+                  description="This file should not be unzipped",
+                  categories=["Test file"]
+            ),
+            File(filepath="tests/fixtures/add_dir_files/somefile.txt",
+                  dv_dir="subdir",
+                  description="A simple text file",
+                  categories=["Test file"]
+            ),
+        ]
+
+        # Act
+        uploader = DVUploader(files=files)
+        uploader.upload(
+            persistent_id=pid,
+            api_token=API_TOKEN,
+            dataverse_url=BASE_URL,
+            n_parallel_uploads=10,
+        )
+
+        # Assert
+        files = retrieve_dataset_files(
+            dataverse_url=BASE_URL,
+            persistent_id=pid,
+            api_token=API_TOKEN,
+        )
+
+        assert len(files) == 2, f"Expected 2 files, got {len(files)}"
+
+        expected_files = [
+            {
+                "label": "archive.zip",
+                "description": "This file should not be unzipped",
+                "categories": ["Test file"]
+            },
+            {
+                "label": "somefile.txt",
+                "description": "A simple text file",
+                "categories": ["Test file"]
+            },
+        ]
+
+        files_as_expected = sorted(
+            [
+                {
+                    k: (f[k] if k in f else None)
+                    for k in expected_files[0].keys()
+                }
+                for f in files
+            ],
+            key=lambda x: x["label"]
+        )
+        assert files_as_expected == expected_files, (
+            f"File metadata not as expected: {json.dumps(files, indent=2)}"
+        )
+
+
     def test_too_many_zip_files(
         self,
         credentials,