diff --git a/dlt/destinations/impl/filesystem/filesystem.py b/dlt/destinations/impl/filesystem/filesystem.py
index 985af6f927..c4fbbaf71a 100644
--- a/dlt/destinations/impl/filesystem/filesystem.py
+++ b/dlt/destinations/impl/filesystem/filesystem.py
@@ -268,7 +268,9 @@ def sql_client(self) -> SqlClientBase[Any]:
         from dlt.destinations.impl.filesystem.sql_client import FilesystemSqlClient
 
         if not self._sql_client:
-            self._sql_client = FilesystemSqlClient(self, protocol=self.config.protocol)
+            self._sql_client = FilesystemSqlClient(
+                self, protocol=self.config.protocol, dataset_name=self.dataset_name
+            )
         return self._sql_client
 
     @sql_client.setter
@@ -705,6 +707,7 @@ def create_table_chain_completed_followup_jobs(
     def table_relation(
         self, *, table: str, columns: TTableSchemaColumns
     ) -> Generator[DBApiCursor, Any, Any]:
+        table = self.sql_client.make_qualified_table_name(table)
         with self.sql_client.execute_query(f"SELECT * FROM {table}") as cursor:
             cursor.columns = columns
             yield cursor
diff --git a/dlt/destinations/impl/filesystem/sql_client.py b/dlt/destinations/impl/filesystem/sql_client.py
index 1b3d1061dc..baf930cd55 100644
--- a/dlt/destinations/impl/filesystem/sql_client.py
+++ b/dlt/destinations/impl/filesystem/sql_client.py
@@ -19,22 +19,25 @@
 
 
 class FilesystemSqlClient(DuckDbSqlClient):
-    def __init__(self, fs_client: FSClientBase, protocol: str) -> None:
+    def __init__(self, fs_client: FSClientBase, protocol: str, dataset_name: str) -> None:
         """For now we do all operations in the memory dataset"""
         """TODO: is this ok?"""
         super().__init__(
-            dataset_name="memory",
+            dataset_name=dataset_name,
             staging_dataset_name=None,
             credentials=None,
             capabilities=duckdb_factory()._raw_capabilities(),
         )
         self.fs_client = fs_client
-        self._conn = duckdb.connect(":memory:")
-        self._conn.register_filesystem(self.fs_client.fs_client)
         self.existing_views: List[str] = []  # remember which views already where created
         self.protocol = protocol
         self.is_local_filesystem = protocol == "file"
 
+        # set up duckdb instance
+        self._conn = duckdb.connect(":memory:")
+        self._conn.sql(f"CREATE SCHEMA {self.dataset_name}")
+        self._conn.register_filesystem(self.fs_client.fs_client)
+
     @raise_database_error
     def populate_duckdb(self, tables: List[str]) -> None:
         """Add the required tables as views to the duckdb in memory instance"""
@@ -60,6 +63,7 @@ def populate_duckdb(self, tables: List[str]) -> None:
             # create table
             protocol = "" if self.is_local_filesystem else f"{self.protocol}://"
             files_string = f"'{protocol}{folder}/**/*.{file_type}'"
+            ptable = self.make_qualified_table_name(ptable)
             create_table_sql_base = (
                 f"CREATE VIEW {ptable} AS SELECT * FROM {read_command}([{files_string}])"
             )