diff --git a/msg/templates/urtps/microRTPS_agent_CMakeLists.txt.em b/msg/templates/urtps/microRTPS_agent_CMakeLists.txt.em
index f5c431e5c0..2f642734f3 100644
--- a/msg/templates/urtps/microRTPS_agent_CMakeLists.txt.em
+++ b/msg/templates/urtps/microRTPS_agent_CMakeLists.txt.em
@@ -50,6 +50,6 @@ if(CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG OR
     endif()
 endif()
 
-file(GLOB MICRORTPS_AGENT_SOURCES *.cpp *.h)
+file(GLOB MICRORTPS_AGENT_SOURCES src/*.cpp src/*.h)
 add_executable(micrortps_agent ${MICRORTPS_AGENT_SOURCES})
 target_link_libraries(micrortps_agent fastrtps fastcdr)
diff --git a/msg/tools/generate_microRTPS_bridge.py b/msg/tools/generate_microRTPS_bridge.py
index 91e6475a17..3314b9caa5 100644
--- a/msg/tools/generate_microRTPS_bridge.py
+++ b/msg/tools/generate_microRTPS_bridge.py
@@ -264,10 +264,10 @@ else:
 # get ROS 2 version, if exists
 ros2_distro = ''
 ros_version = os.environ.get('ROS_VERSION')
-if ros_version == '2' :
+if ros_version == '2':
     if args.ros2_distro != '':
         ros2_distro = args.ros2_distro
-    else :
+    else:
         ros2_distro = os.environ.get('ROS_DISTRO')
 
 # get FastRTPS version
@@ -414,7 +414,7 @@ def generate_agent(out_dir):
     px_generate_uorb_topic_files.generate_uRTPS_general(classifier.msgs_to_send, classifier.alias_msgs_to_send, classifier.msgs_to_receive, classifier.alias_msgs_to_receive, msg_dir, out_dir,
                                                         urtps_templates_dir, package, px_generate_uorb_topic_files.INCL_DEFAULT, classifier.msg_id_map, fastrtps_version, ros2_distro, uRTPS_AGENT_TOPICS_SRC_TEMPL_FILE)
     if cmakelists:
-        px_generate_uorb_topic_files.generate_uRTPS_general(classifier.msgs_to_send, classifier.alias_msgs_to_send, classifier.msgs_to_receive, classifier.alias_msgs_to_receive, msg_dir, out_dir,
+        px_generate_uorb_topic_files.generate_uRTPS_general(classifier.msgs_to_send, classifier.alias_msgs_to_send, classifier.msgs_to_receive, classifier.alias_msgs_to_receive, msg_dir, os.path.dirname(out_dir),
                                                             urtps_templates_dir, package, px_generate_uorb_topic_files.INCL_DEFAULT, classifier.msg_id_map, fastrtps_version, ros2_distro, uRTPS_AGENT_CMAKELISTS_TEMPL_FILE)
 
     # Final steps to install agent
@@ -450,10 +450,10 @@ def generate_agent(out_dir):
     cp_wildcard(os.path.join(urtps_templates_dir,
                              "microRTPS_transport.*"), agent_out_dir)
     if cmakelists:
-        os.rename(os.path.join(out_dir, "microRTPS_agent_CMakeLists.txt"),
-                  os.path.join(out_dir, "CMakeLists.txt"))
+        os.rename(os.path.join(os.path.dirname(out_dir), "microRTPS_agent_CMakeLists.txt"),
+                  os.path.join(os.path.dirname(out_dir), "CMakeLists.txt"))
     if (mkdir_build):
-        mkdir_p(os.path.join(out_dir, "build"))
+        mkdir_p(os.path.join(os.path.dirname(out_dir), "build"))
     os.chdir(prev_cwd_path)
     return 0
 
diff --git a/src/modules/micrortps_bridge/micrortps_client/CMakeLists.txt b/src/modules/micrortps_bridge/micrortps_client/CMakeLists.txt
index 3d74fbc57a..b1264a7bf3 100644
--- a/src/modules/micrortps_bridge/micrortps_client/CMakeLists.txt
+++ b/src/modules/micrortps_bridge/micrortps_client/CMakeLists.txt
@@ -32,6 +32,7 @@
 ############################################################################
 
 set(msg_out_path ${CMAKE_CURRENT_BINARY_DIR})
+get_filename_component(micrortps_bridge_path ${msg_out_path} PATH)
 
 if (NOT "${config_rtps_send_topics}" STREQUAL "" OR NOT "${config_rtps_receive_topics}" STREQUAL "")
 
@@ -54,19 +55,19 @@ if (NOT "${config_rtps_send_topics}" STREQUAL "" OR NOT "${config_rtps_receive_t
 	endif()
 
 	foreach(topic ${config_rtps_send_topics})
-		list(APPEND topic_bridge_files_out ${msg_out_path}/micrortps_agent/${topic}_Publisher.cpp)
-		list(APPEND topic_bridge_files_out ${msg_out_path}/micrortps_agent/${topic}_Publisher.h)
+		list(APPEND topic_bridge_files_out ${micrortps_bridge_path}/micrortps_agent/${topic}_Publisher.cpp)
+		list(APPEND topic_bridge_files_out ${micrortps_bridge_path}/micrortps_agent/${topic}_Publisher.h)
 	endforeach()
 
 	foreach(topic ${config_rtps_receive_topics})
-		list(APPEND topic_bridge_files_out ${msg_out_path}/micrortps_agent/${topic}_Subscriber.cpp)
-		list(APPEND topic_bridge_files_out ${msg_out_path}/micrortps_agent/${topic}_Subscriber.h)
+		list(APPEND topic_bridge_files_out ${micrortps_bridge_path}/micrortps_agent/${topic}_Subscriber.cpp)
+		list(APPEND topic_bridge_files_out ${micrortps_bridge_path}/micrortps_agent/${topic}_Subscriber.h)
 	endforeach()
 
 	list(APPEND topic_bridge_files_out
-		${msg_out_path}/micrortps_client/microRTPS_client.cpp
-		${msg_out_path}/micrortps_client/microRTPS_transport.cpp
-		${msg_out_path}/micrortps_client/microRTPS_transport.h
+		${micrortps_bridge_path}/micrortps_client/microRTPS_client.cpp
+		${micrortps_bridge_path}/micrortps_client/microRTPS_transport.cpp
+		${micrortps_bridge_path}/micrortps_client/microRTPS_transport.h
 		)
 
 	add_custom_command(OUTPUT ${topic_bridge_files_out}
@@ -78,9 +79,9 @@ if (NOT "${config_rtps_send_topics}" STREQUAL "" OR NOT "${config_rtps_receive_t
 			--topic-msg-dir ${PX4_SOURCE_DIR}/msg
 			--uorb-templates-dir templates/uorb_microcdr
 			--urtps-templates-dir templates/urtps
-			--agent-outdir ${CMAKE_CURRENT_BINARY_DIR}/micrortps_agent
-			--client-outdir ${CMAKE_CURRENT_BINARY_DIR}/micrortps_client
-			--idl-dir ${CMAKE_CURRENT_BINARY_DIR}/micrortps_agent/idl
+			--agent-outdir ${micrortps_bridge_path}/micrortps_agent/src
+			--client-outdir ${micrortps_bridge_path}/micrortps_client
+			--idl-dir ../micrortps_agent/idl
 			>micrortps_bridge.log >/dev/null
 		DEPENDS ${send_topic_files} ${receive_topic_files}
 		COMMENT "Generating RTPS topic bridge"
@@ -93,11 +94,11 @@ if (NOT "${config_rtps_send_topics}" STREQUAL "" OR NOT "${config_rtps_receive_t
 		STACK_MAIN 4096
 		INCLUDES
 			${CMAKE_CURRENT_SOURCE_DIR}
-			${CMAKE_CURRENT_BINARY_DIR}/micrortps_client
+			${micrortps_bridge_path}/micrortps_client
 		SRCS
 			microRTPS_client_main.cpp
-			${msg_out_path}/micrortps_client/microRTPS_client.cpp
-			${msg_out_path}/micrortps_client/microRTPS_transport.cpp
+			${micrortps_bridge_path}/micrortps_client/microRTPS_client.cpp
+			${micrortps_bridge_path}/micrortps_client/microRTPS_transport.cpp
 		MODULE_CONFIG
 			module.yaml
 		DEPENDS