A new variant of the classic capacitated facility location problem, which considers incompatibilities between customers, has recently been introduced in the literature. This problem captures the situation where given pairs of customers cannot be served by the same facility. Such a feature is crucial for many practical cases of location problems, such as the presence of hazardous or polluting materials and contention between competing costumers. In this paper, we propose a Large Neighborhood Search (LNS) method to solve this problem. Within the framework of LNS, we introduce three different destroy operators, which are combined in a hybrid manner, and we use an exact solver in the repair phase. Different algorithmic components are investigated for the design of LNS. The experimental analysis shows that our new method outperforms existing state-of-the-art metaheuristics, providing new best solutions for all available benchmark instances.