diff --git a/pydropsonde/helper/quality.py b/pydropsonde/helper/quality.py
index f4fd60e1..b4c62b92 100644
--- a/pydropsonde/helper/quality.py
+++ b/pydropsonde/helper/quality.py
@@ -437,19 +437,21 @@ def get_details(self, variable):
             )
         return self.qc_by_var.get(variable).get("qc_details"), attrs
 
-    def add_variable_flags_to_ds(self, ds, variable, details=True):
+    def add_variable_flags_to_ds(self, ds, variable, add_to=None, details=True):
+        if add_to is None:
+            add_to = variable
         name = f"{variable}_qc"
         value, attrs = self.get_byte_array(variable)
         ds = ds.assign({name: value})
         ds[name].attrs.update(attrs)
-        ds = hx.add_ancillary_var(ds, variable, name)
+        ds = hx.add_ancillary_var(ds, add_to, name)
         # get detail
         if details:
             qc_dict, attrs = self.get_details(variable)
             for key in list(qc_dict.keys()):
                 ds = ds.assign({key: qc_dict.get(key)})
                 ds[key].attrs.update(attrs.get(key))
-                ds = hx.add_ancillary_var(ds, variable, key)
+                ds = hx.add_ancillary_var(ds, add_to, key)
 
         return ds
 
diff --git a/pydropsonde/pipeline.py b/pydropsonde/pipeline.py
index 7e6569be..5052757b 100644
--- a/pydropsonde/pipeline.py
+++ b/pydropsonde/pipeline.py
@@ -542,8 +542,6 @@ def run_pipeline(pipeline: dict, config: configparser.ConfigParser):
             "remove_non_mono_incr_alt",
             "swap_alt_dimension",
             "interpolate_alt",
-            "get_N_m_values",
-            "add_Nm_to_vars",
             "recalc_rh_and_ta",
             "add_iwv",
             "add_ids",
@@ -551,6 +549,8 @@ def run_pipeline(pipeline: dict, config: configparser.ConfigParser):
             "add_attributes_as_var",
             "make_attr_coordinates",
             "add_qc_to_interim_l3",
+            "get_N_m_values",
+            "add_Nm_to_vars",
             "add_globals_l3",
             "add_expected_coords",
             "save_interim_l3",
diff --git a/pydropsonde/processor.py b/pydropsonde/processor.py
index d73158f8..f6d273e4 100644
--- a/pydropsonde/processor.py
+++ b/pydropsonde/processor.py
@@ -1496,7 +1496,7 @@ def make_attr_coordinates(self):
         self.interim_l3_ds = ds.assign_coords(new_coords)
         return self
 
-    def add_qc_to_interim_l3(self, keep=["sonde_qc"]):
+    def add_qc_to_interim_l3(self, keep=None):
         """
         Add quality control flags to the interim Level 3 dataset.
 
@@ -1510,6 +1510,7 @@ def add_qc_to_interim_l3(self, keep=["sonde_qc"]):
         Returns:
             self: The instance with updated `interim_l3_ds` including quality control flags.
         """
+        ds = self.interim_l3_ds
         if keep is None:
             keep = []
         elif keep == "all":
@@ -1518,11 +1519,35 @@ def add_qc_to_interim_l3(self, keep=["sonde_qc"]):
                 + list(self.qc.qc_details.keys())
                 + ["low_physics", "alt_near_gpsalt"]
             )
-        elif isinstance(keep, str):
-            keep = keep.split(",")
-        keep = keep + ["sonde_id"]
+        else:
+            for var in ds.variables:
+                if var != "sonde_id":
+                    ds[var].attrs.pop("ancillary_variables", None)
+            if keep is None:
+                keep = []
+            elif keep == "var_flags":
+                keep = [f"{var}_qc" for var in list(self.qc.qc_by_var.keys())] + [
+                    "sonde_qc"
+                ]
+                for var in self.qc.qc_by_var.keys():
+                    ds = hx.add_ancillary_var(ds, var, var + "_qc")
+                if (not np.isin("q", self.qc.qc_vars)) and np.isin(
+                    "rh", self.qc.qc_vars
+                ):
+                    ds = hx.add_ancillary_var(ds, "q", "rh_qc")
+                if (not np.isin("theta", self.qc.qc_vars)) and np.isin(
+                    "ta", self.qc.qc_vars
+                ):
+                    ds = hx.add_ancillary_var(ds, "theta", "ta_qc")
+
+            else:
+                warnings.warn(
+                    "your keep argument for the qc flags in level 3 is not valid, no qc added"
+                )
+                keep = []
+        keep = keep + ["sonde_qc"]
         ds_qc = self.interim_l2_ds[keep].expand_dims("sonde_id")
-        self.interim_l3_ds = xr.merge([self.interim_l3_ds, ds_qc])
+        self.interim_l3_ds = xr.merge([ds, ds_qc])
 
         return self