2,3,4,5,6-Pentafluorobenzylphosphonic acid is primarily used in organic synthesis and material science. Its unique structure makes it valuable for modifying surfaces, particularly in the development of advanced coatings and films. The compound is often employed as a building block in the creation of phosphonate-based materials, which are known for their stability and resistance to harsh conditions. In addition, it finds applications in the preparation of metal-organic frameworks (MOFs) and other porous materials, where it helps in tuning the properties for specific uses like gas storage or catalysis. The pentafluorobenzyl group enhances its reactivity, making it useful in coupling reactions and as a ligand in coordination chemistry.