diff --git a/tests/providers/s3/test_provider.py b/tests/providers/s3/test_provider.py
index ddee6756d..1b7498675 100644
--- a/tests/providers/s3/test_provider.py
+++ b/tests/providers/s3/test_provider.py
@@ -257,6 +257,21 @@ async def test_validate_v1_path_file(self, provider, file_header_metadata, mock_
 
         assert wb_path_v1 == wb_path_v0
 
+    @pytest.mark.asyncio
+    @pytest.mark.aiohttpretty
+    async def test_validate_v1_path_file_with_subfolder(self, provider, file_header_metadata, mock_time):
+        file_path = '/my-subfolder/foobah'
+        provider.settings['id'] = 'the-bucket:/my-subfolder/'
+
+        good_metadata_url = provider.bucket.new_key(file_path).generate_url(100, 'HEAD')
+        aiohttpretty.register_uri('HEAD', good_metadata_url, headers=file_header_metadata)
+
+        assert WaterButlerPath('/my-subfolder/') == await provider.validate_v1_path('/')
+        wb_path_v1 = await provider.validate_v1_path(file_path)
+        wb_path_v0 = await provider.validate_path(file_path)
+
+        assert wb_path_v1 == wb_path_v0
+
     @pytest.mark.asyncio
     @pytest.mark.aiohttpretty
     async def test_validate_v1_path_folder(self, provider, folder_metadata, mock_time):
@@ -408,6 +423,35 @@ async def test_download_folder_400s(self, provider, mock_time):
             await provider.download(WaterButlerPath('/cool/folder/mom/'))
         assert e.value.code == 400
 
+    @pytest.mark.asyncio
+    @pytest.mark.aiohttpretty
+    async def test_upload_to_subfolder_as_root(self,
+                                               provider,
+                                               file_content,
+                                               file_stream,
+                                               file_header_metadata,
+                                               mock_time
+                                               ):
+
+        provider.settings['id'] = 'the-bucket:/my-subfolder/'
+        path = WaterButlerPath('/my-subfolder/foobah')
+
+        content_md5 = hashlib.md5(file_content).hexdigest()
+
+        url = provider.bucket.new_key(path.path).generate_url(100, 'PUT')
+        metadata_url = provider.bucket.new_key(path.path).generate_url(100, 'HEAD')
+        aiohttpretty.register_uri('HEAD', metadata_url, headers=file_header_metadata)
+        header = {'ETag': f'"{content_md5}"'}
+        aiohttpretty.register_uri('PUT', url, status=201, headers=header)
+
+        metadata, created = await provider.upload(file_stream, path)
+
+        assert metadata.kind == 'file'
+        assert metadata.path == '/my-subfolder/foobah'
+        assert not created
+        assert aiohttpretty.has_call(method='PUT', uri=url)
+        assert aiohttpretty.has_call(method='HEAD', uri=metadata_url)
+
     @pytest.mark.asyncio
     @pytest.mark.aiohttpretty
     async def test_upload_update(self,
diff --git a/waterbutler/providers/s3/provider.py b/waterbutler/providers/s3/provider.py
index a2419f7f1..dd3ac664f 100644
--- a/waterbutler/providers/s3/provider.py
+++ b/waterbutler/providers/s3/provider.py
@@ -688,7 +688,11 @@ async def _metadata_file(self, path, revision=None):
     async def _metadata_folder(self, path):
         await self._check_region()
 
-        params = {'prefix': path.path, 'delimiter': '/'}
+        # The user selected base folder, the root of the where that user's node is connected.
+        prefix = self.settings['id'].split(':/')[1] if path == '/' and self.settings.get('id') else path.path
+
+        params = {'prefix': prefix, 'delimiter': '/'}
+
         resp = await self.make_request(
             'GET',
             functools.partial(self.bucket.generate_url, settings.TEMP_URL_SECS, 'GET', query_parameters=params),
@@ -731,11 +735,11 @@ async def _metadata_folder(self, path):
 
         items = [
             S3FolderMetadata(item)
-            for item in prefixes
+            for item in prefixes if item['Prefix'] != path.path
         ]
 
         for content in contents:
-            if content['Key'] == path.path:
+            if content['Key'] == params['prefix']:
                 continue
 
             if content['Key'].endswith('/'):