diff --git a/build-tools/build-helm-charts.sh b/build-tools/build-helm-charts.sh
index 29b1f6cc..35c5a5be 100755
--- a/build-tools/build-helm-charts.sh
+++ b/build-tools/build-helm-charts.sh
@@ -302,9 +302,34 @@ function build_application_tarball_armada {
     fi
 }
 
+function compare_custom_manifests {
+    MANIFEST_LIST=$1
+    for manifest in ${MANIFEST_LIST}; do
+        MAIN_MANIFESTS=$(ls usr/lib/fluxcd/${manifest})
+        CUSTOM_MANIFESTS=$(ls usr/lib/fluxcd/custom-manifests/${manifest})
+
+        for manifest_file in ${MAIN_MANIFESTS}; do
+            if [ ! -f usr/lib/fluxcd/custom-manifests/${manifest}/${manifest_file} ]; then
+                echo "Warning: missing ${manifest_file} in custom manifests"
+            else
+                ${PYTHON_2_OR_3} $BUILD_HELM_CHARTS_DIR/merge_manifests.py usr/lib/fluxcd/${manifest}/${manifest_file} usr/lib/fluxcd/custom-manifests/${manifest}/${manifest_file}
+            fi
+        done
+    done
+}
+
 function build_application_tarball_fluxcd {
 
     FLUXCD_MANIFEST_DIR='fluxcd-manifests'
+    CUSTOM_MANIFEST_LIST=$(ls usr/lib/fluxcd/custom-manifests)
+
+    if [ ${#CUSTOM_MANIFEST_LIST} -ne 0 ]; then
+        echo "Custom manifests detected. Merging custom manifests with FluxCD manifests"
+        compare_custom_manifests "${CUSTOM_MANIFEST_LIST}"
+
+        # Removing custom manifests directory to prevent unnecessary files from being included
+        rm -rd usr/lib/fluxcd/custom-manifests
+    fi
 
     # Stage all the fluxcd manifests
     cp -R usr/lib/fluxcd staging/${FLUXCD_MANIFEST_DIR}
diff --git a/build-tools/merge_manifests.py b/build-tools/merge_manifests.py
new file mode 100644
index 00000000..0031f67b
--- /dev/null
+++ b/build-tools/merge_manifests.py
@@ -0,0 +1,48 @@
+#!/usr/bin/python
+#
+# Copyright (c) 2024 Wind River Systems, Inc.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
+import os
+import sys
+import ruamel.yaml as yaml
+
+def merge_dicts(main: dict, custom: dict) -> None:
+    for key, value in custom.items():
+        if key in main and isinstance(main[key], dict) and isinstance(value, dict):
+            merge_dicts(main[key], value)
+        else:
+            main[key] = value
+
+def handle_manifests_merge(main_manifests_path: str, custom_manifests_path: str):
+    with open(main_manifests_path, 'r') as main_file, open(custom_manifests_path, 'r') as custom_file:
+        main_data = yaml.safe_load(main_file)
+        custom_data = yaml.safe_load(custom_file)
+
+    # If both main file data and custom data are identical, no merge is needed
+    if main_data == custom_data:
+        return
+
+    # Handle empty YAML files as empty dictionaries for comparison purposes
+    main_data = {} if main_data is None else main_data
+    custom_data = {} if custom_data is None else custom_data
+
+    merged_data = main_data.copy()
+
+    merge_dicts(merged_data, custom_data)
+
+    with open(main_manifests_path, 'w') as main_file:
+        yaml.dump(merged_data, main_file, default_flow_style=False)
+
+if __name__ == "__main__":
+
+    main_manifests_path = sys.argv[1]
+    custom_manifests_path = sys.argv[2]
+
+    try:
+        handle_manifests_merge(main_manifests_path, custom_manifests_path)
+    except Exception as e:
+        print(f"Error trying to merge {main_manifests_path}: {e}")
+        sys.exit(1)