diff --git a/soda/core/soda/execution/check/row_count_comparison_check.py b/soda/core/soda/execution/check/row_count_comparison_check.py
index 03cdbaee5..9adc4f0ad 100644
--- a/soda/core/soda/execution/check/row_count_comparison_check.py
+++ b/soda/core/soda/execution/check/row_count_comparison_check.py
@@ -26,6 +26,7 @@ def __init__(
         )
 
         data_source_scan = self.data_source_scan
+        data_source_scan_cfg = self.data_source_scan.data_source_scan_cfg
         scan = data_source_scan.scan
 
         row_count_comparison_check_cfg: RowCountComparisonCheckCfg = self.check_cfg
@@ -38,6 +39,16 @@ def __init__(
         other_table: Table = data_source_scan.get_or_create_table(row_count_comparison_check_cfg.other_table_name)
         self.other_partition = other_table.get_or_create_partition(row_count_comparison_check_cfg.other_partition_name)
 
+        # If the other partition is None, we ignore the partition_cfg setup
+        if row_count_comparison_check_cfg.other_partition_name:
+            other_table_cfg = data_source_scan_cfg.get_or_create_table_cfg(
+                row_count_comparison_check_cfg.other_table_name
+            )
+            other_partition_cfg = other_table_cfg.find_partition(
+                row_count_comparison_check_cfg.location.file_path, row_count_comparison_check_cfg.other_partition_name
+            )
+            self.other_partition.set_partition_cfg(other_partition_cfg)
+
         self.metrics["row_count"] = self.data_source_scan.resolve_metric(
             NumericQueryMetric(
                 data_source_scan=self.data_source_scan,
diff --git a/soda/core/tests/data_source/test_row_count_comparison.py b/soda/core/tests/data_source/test_row_count_comparison.py
index c117faae0..9186b3386 100644
--- a/soda/core/tests/data_source/test_row_count_comparison.py
+++ b/soda/core/tests/data_source/test_row_count_comparison.py
@@ -61,3 +61,34 @@ def test_row_count_comparison_cross_data_source(data_source_fixture: DataSourceF
     scan.execute()
 
     scan.assert_all_checks_pass()
+
+
+def test_row_count_comparison_cross_data_source_with_filter(data_source_fixture: DataSourceFixture):
+    """Does not really create two connections and test cross data sources with filtering, that is handled in integration tests.
+
+    Tests syntax parsing and check execution.
+    """
+    customers_table_name = data_source_fixture.ensure_test_table(customers_test_table)
+    rawcustomers_table_name = data_source_fixture.ensure_test_table(raw_customers_test_table)
+
+    # Reuse the same data source name
+    other_data_source_name = data_source_fixture.data_source.data_source_name
+
+    scan = data_source_fixture.create_test_scan()
+    scan.add_sodacl_yaml_str(
+        f"""
+            filter {customers_table_name} [daily]:
+              where: cst_size IS NULL
+
+            filter {rawcustomers_table_name} [daily-ref]:
+              where: cst_size IS NULL
+
+            checks for {customers_table_name} [daily]:
+              - row_count same as {rawcustomers_table_name} daily-ref in {other_data_source_name}
+        """
+    )
+
+    scan.execute()
+    print(scan.get_passing_queries())
+
+    scan.assert_all_checks_pass()