Multispectral images allow the identification of crop conditions that can be used for proper decision making in agriculture activities. A multispectral imaging system that includes cameras mounted on an Unmanned Aerial Vehicle (UAV) with other electronic modules such as GPS and autopilot system has been developed for covering great extensions of land and the acquisition of geolocated images. However, image resolution limits the altitude at which the UAV can fly and the image acquisition rate. Therefore, an integral design among the embedded system, digital cameras and trigger interface must be developed in order to guarantee an acceptable performance. This paper provides a design proposition for a multispectral system for interfacing with an onboard flight controller to synchronize data acquisition and obtain aerial images.