This article presents the deployment of micro UAVs to study the evolution of cumulus clouds. The dynamic nature of the environment, the difficult weather conditions, the long distances, and the limited flight performances of micro UAV systems make such missions quite challenging. After describing the missions constraints and objectives, the system's main component is depicted: it is the definition of adaptive flight patterns that allow the UAVs to track the areas of interest in the clouds autonomously, using real-time sensor readings. The system architecture is then presented, considering the information feedback and decision process made by the operators and scientists on the ground and the necessary flight autonomy of the UAVs. The complete system has been deployed during an international meteorological campaign on Barbados island, and extended with extra test flights afterward. Details of the operational organization and the achieved flights are reported. The lessons learned during the field campaign revealed the strength and weaknesses of the proposed system and possible improvements are discussed. The collected data has contributed to a better understanding of cloud evolution, demonstrating that a tight coupling of the sensors and the flight control system is a crucial point for extending the performances of UAV systems in atmospheric science.