diff --git a/cosmos/dbt/graph.py b/cosmos/dbt/graph.py
index 0d26a32644..d25f0d44a7 100644
--- a/cosmos/dbt/graph.py
+++ b/cosmos/dbt/graph.py
@@ -8,6 +8,7 @@
 import os
 import platform
 import tempfile
+import warnings
 import zlib
 from dataclasses import dataclass, field
 from functools import cached_property
@@ -836,6 +837,11 @@ def load_via_custom_parser(self) -> None:
         * self.filtered_nodes
         """
         self.load_method = LoadMode.CUSTOM
+        warnings.warn(
+            "Using `load_method` = `LoadMode.CUSTOM` is deprecated in current version and will"
+            " be removed in Cosmos 2.0",
+            DeprecationWarning,
+        )
         logger.info("Trying to parse the dbt project `%s` using a custom Cosmos method...", self.project.project_name)
 
         if self.render_config.selector:
diff --git a/tests/dbt/test_graph.py b/tests/dbt/test_graph.py
index 8b0522ea10..4b125bf471 100644
--- a/tests/dbt/test_graph.py
+++ b/tests/dbt/test_graph.py
@@ -1041,6 +1041,31 @@ def test_load_via_load_via_custom_parser(project_name, nodes_count):
     assert len(dbt_graph.nodes) == nodes_count
 
 
+@pytest.mark.parametrize("project_name", [("altered_jaffle_shop"), ("jaffle_shop_python")])
+def test_validate_load_via_load_via_custom_parser_deprecated(project_name):
+    """Deprecating warnings should be raised when using load_mode CUSTOM."""
+    project_config = ProjectConfig(dbt_project_path=DBT_PROJECTS_ROOT_DIR / project_name)
+    execution_config = ExecutionConfig(dbt_project_path=DBT_PROJECTS_ROOT_DIR / project_name)
+    render_config = RenderConfig(
+        dbt_project_path=DBT_PROJECTS_ROOT_DIR / project_name,
+        source_rendering_behavior=SOURCE_RENDERING_BEHAVIOR,
+    )
+    profile_config = ProfileConfig(
+        profile_name="test",
+        target_name="test",
+        profiles_yml_filepath=DBT_PROJECTS_ROOT_DIR / project_name / "profiles.yml",
+    )
+    dbt_graph = DbtGraph(
+        project=project_config,
+        profile_config=profile_config,
+        render_config=render_config,
+        execution_config=execution_config,
+    )
+
+    with pytest.deprecated_call():
+        dbt_graph.load_via_custom_parser()
+
+
 def test_load_via_load_via_custom_parser_select_rendering_config():
     project_config = ProjectConfig(dbt_project_path=DBT_PROJECTS_ROOT_DIR / "jaffle_shop")
     execution_config = ExecutionConfig(dbt_project_path=DBT_PROJECTS_ROOT_DIR / DBT_PROJECT_NAME)