diff --git a/benchmarks/holoscan_flow_benchmarking/README.md b/benchmarks/holoscan_flow_benchmarking/README.md
index 36fea8d81..e0fe8050b 100644
--- a/benchmarks/holoscan_flow_benchmarking/README.md
+++ b/benchmarks/holoscan_flow_benchmarking/README.md
@@ -45,8 +45,7 @@ This script saves the original `cpp` files in a `*.cpp.bak` file.
 2. **Build the application**
 
 ```
-$ ./run build <application name> <other options> \
-    --configure-args -DCMAKE_CXX_FLAGS=-I$PWD/benchmarks/holoscan_flow_benchmarking
+$ ./run build <application name> <other options> --benchmark
 ```
 
 Please make sure to test that the application runs correctly after building it, and before going to
diff --git a/run b/run
index f65e405f5..b1cba87f5 100755
--- a/run
+++ b/run
@@ -681,6 +681,12 @@ build() {
     build_path="build/$1"
   fi
 
+  local app_source_root_path
+  if [ $benchmark == true ]; then
+    app_source_root_path=$(get_app_source_root_dir $1)
+    run_command benchmarks/holoscan_flow_benchmarking/patch_application.sh ${app_source_root_path}
+  fi
+
   echo "Building $1 application"
   application="-DAPP_$1=1"
 
@@ -699,6 +705,11 @@ build() {
   ret=$?
   check_exit_code $ret "Error building application."
 
+  if [ $benchmark == true ]; then
+    app_source_root_path=$(get_app_source_root_dir $1)
+    run_command benchmarks/holoscan_flow_benchmarking/restore_application.sh ${app_source_root_path}
+  fi
+
   echo "Holohub build done."
 }