diff --git a/looper/const.py b/looper/const.py
index e25f911f..017aceb4 100644
--- a/looper/const.py
+++ b/looper/const.py
@@ -95,6 +95,7 @@
     "LOOPER_GENERIC_OUTPUT_SCHEMA",
     "LOOPER_GENERIC_COUNT_LINES",
     "CLI_MODS_KEY",
+    "PipelineLevel",
 ]
 
 FLAGS = ["completed", "running", "failed", "waiting", "partial"]
diff --git a/looper/utils.py b/looper/utils.py
index 9cc8eeaa..6e052f96 100644
--- a/looper/utils.py
+++ b/looper/utils.py
@@ -17,6 +17,7 @@
 from ubiquerg import convert_value, expandpath, parse_registry_path, deep_update
 from pephubclient.constants import RegistryPath
 from pydantic import ValidationError
+from yacman import load_yaml
 
 from .const import *
 from .command_models.commands import SUPPORTED_COMMANDS
@@ -534,6 +535,33 @@ def initiate_looper_config(
     return True
 
 
+def determine_pipeline_type(piface_path: str, looper_config_path: str):
+    """
+    Read pipeline interface from disk and determine if pipeline type is sample or project-level
+
+
+    :param str piface_path: path to pipeline_interface
+    :param str looper_config_path: path to looper config file
+    :return Tuple[Union[str,None],Union[str,None]] : (pipeline type, resolved path) or (None, None)
+    """
+
+    if piface_path is None:
+        return None, None
+    piface_path = expandpath(piface_path)
+    if not os.path.isabs(piface_path):
+        piface_path = os.path.realpath(
+            os.path.join(os.path.dirname(looper_config_path), piface_path)
+        )
+    try:
+        piface_dict = load_yaml(piface_path)
+    except FileNotFoundError:
+        return None, None
+
+    pipeline_type = piface_dict.get("pipeline_type", None)
+
+    return pipeline_type, piface_path
+
+
 def read_looper_config_file(looper_config_path: str) -> dict:
     """
     Read Looper config file which includes:
@@ -581,11 +609,39 @@ def read_looper_config_file(looper_config_path: str) -> dict:
         return_dict[CLI_MODS_KEY] = dp_data[CLI_MODS_KEY]
 
     if PIPELINE_INTERFACES_KEY in dp_data:
+
         dp_data.setdefault(PIPELINE_INTERFACES_KEY, {})
-        return_dict[SAMPLE_PL_ARG] = dp_data.get(PIPELINE_INTERFACES_KEY).get("sample")
-        return_dict[PROJECT_PL_ARG] = dp_data.get(PIPELINE_INTERFACES_KEY).get(
-            "project"
-        )
+
+        if isinstance(dp_data.get(PIPELINE_INTERFACES_KEY), dict) and (
+            dp_data.get(PIPELINE_INTERFACES_KEY).get("sample")
+            or dp_data.get(PIPELINE_INTERFACES_KEY).get("project")
+        ):
+            # Support original nesting of pipeline interfaces under "sample" and "project"
+            return_dict[SAMPLE_PL_ARG] = dp_data.get(PIPELINE_INTERFACES_KEY).get(
+                "sample"
+            )
+            return_dict[PROJECT_PL_ARG] = dp_data.get(PIPELINE_INTERFACES_KEY).get(
+                "project"
+            )
+        else:
+            # infer pipeline type based from interface instead of nested keys: https://github.com/pepkit/looper/issues/465
+            all_pipeline_interfaces = dp_data.get(PIPELINE_INTERFACES_KEY)
+            sample_pifaces = []
+            project_pifaces = []
+            if isinstance(all_pipeline_interfaces, str):
+                all_pipeline_interfaces = [all_pipeline_interfaces]
+            for piface in all_pipeline_interfaces:
+                pipeline_type, piface_path = determine_pipeline_type(
+                    piface, looper_config_path
+                )
+                if pipeline_type == PipelineLevel.SAMPLE.value:
+                    sample_pifaces.append(piface_path)
+                elif pipeline_type == PipelineLevel.PROJECT.value:
+                    project_pifaces.append(piface_path)
+            if len(sample_pifaces) > 0:
+                return_dict[SAMPLE_PL_ARG] = sample_pifaces
+            if len(project_pifaces) > 0:
+                return_dict[PROJECT_PL_ARG] = project_pifaces
 
     else:
         _LOGGER.warning(