Over the last few decades, we witnessed a revolution in acquiring very high resolution and accurate geo-information. One of the reasons was the advances in photonics and LiDAR, which had a remarkable impact in applications requiring information with high accuracy and/or elevated completeness, such as flood modelling, forestry, construction, and mining. Also, miniaturization within electronics played an important role as it allowed smaller and lighter aerial cameras and LiDAR systems to be carried by unmanned aerial vehicles (UAV). While the use of aerial imagery acquired with UAV is becoming a standard procedure in geo-information extraction for several applications, the use of LiDAR for this purpose is still in its infancy. In several countries, companies have started to commercialize products derived from LiDAR data acquired using a UAV but not always with the necessary expertise and experience. The LIDAR-derived products’ price has become very attractive, but their quality must meet the contracted specifications. Few studies have reported on the quality of outsourced LiDAR data acquired with UAV and the problems that need to be handled during production. There can be significant differences between the planning and execution of a commercial project and a research field campaign, particularly concerning the size of the surveyed area, the volume of the acquired data, and the strip processing. This work addresses the quality control of LiDAR UAV data through outsourcing to develop a modelling-based flood forecast and alert system. The contracted company used the Phoenix Scout-16 from Phoenix LiDAR Systems, carrying a Velodyne VLP-16 and mounted on a DJI Matrice 600 PRO Hexacopter for an area of 560 ha along a flood-prone area of the Águeda River in Central Portugal.