diff --git a/riocli/apply/parse.py b/riocli/apply/parse.py
index 1e86574f..ee594be1 100644
--- a/riocli/apply/parse.py
+++ b/riocli/apply/parse.py
@@ -18,6 +18,7 @@
 
 import click
 import yaml
+from benedict import benedict
 from graphlib import TopologicalSorter
 from munch import munchify
 
@@ -28,7 +29,7 @@
     print_resolved_objects,
 )
 from riocli.config import Configuration
-from riocli.constants import Colors, Symbols, ApplyResult
+from riocli.constants import ApplyResult, Colors, Symbols
 from riocli.exceptions import ResourceNotFound
 from riocli.utils import dump_all_yaml, print_centered_text, run_bash
 from riocli.utils.graph import Graphviz
@@ -488,7 +489,7 @@ def _inject_rio_namespace(self, values: typing.Optional[dict] = None) -> dict:
         }
 
         if "rio" in values:
-            values["rio"].update(rio)
+            benedict(values["rio"]).merge(rio)
         else:
             values["rio"] = rio
 
@@ -498,15 +499,15 @@ def _process_values_and_secrets(
         self, values: typing.List, secrets: typing.List
     ) -> None:
         """Process the values and secrets files and inject them into the manifest files"""
-        self.values, self.secrets = {}, {}
+        self.values, self.secrets = benedict({}), benedict({})
 
         values = values or []
         secrets = secrets or []
 
         for v in values:
-            self.values.update(self._load_file_content(v, is_value=True)[0])
+            benedict(self.values).merge(self._load_file_content(v, is_value=True)[0])
 
         self.values = self._inject_rio_namespace(self.values)
 
         for s in secrets:
-            self.secrets.update(self._load_file_content(s, is_secret=True)[0])
+            benedict(self.values).merge(self._load_file_content(s, is_secret=True)[0])
diff --git a/uv.lock b/uv.lock
index 62298082..0ec11e68 100644
--- a/uv.lock
+++ b/uv.lock
@@ -721,7 +721,7 @@ wheels = [
 
 [[package]]
 name = "rapyuta-io-cli"
-version = "0.0.0"
+version = "9.0.4"
 source = { editable = "." }
 dependencies = [
     { name = "argparse" },