This paper presents a novel version control system for point clouds, which allows the complete editing history of a dataset to be stored. For each intermediate version, this system stores only the information that changes with respect to the previous one, which is compressed using a new strategy based on several algorithms. It allows undo/redo functionality in memory, which serves to optimize the operation of the version control system. It can also manage changes produced from third-party applications, which makes it ideal to be integrated into typical Computer-Aided Design workflows. In addition to automated management of incremental versions of point cloud datasets, the proposed system has a much lower storage footprint than the manual backup approach for most common point cloud workflows, which is essential when working with LiDAR (Light Detection and Ranging) data in the context of spatial big data.