Peri-implantitis remains the major impediment to the long-term use of dental implants. With increasing concern over the growth in antibiotic resistance, there is considerable interest in the preparation of antimicrobial dental implant coatings that also induce osseointegration. One such potential coating material is fluorapatite (FA). The aim of this study was to relate the antibacterial effectiveness of FA coatings against pathogens implicated in peri-implantitis to the physicochemical properties of the coating. Ordered and disordered FA coatings were produced on the under and upper surfaces of stainless steel (SS) discs, respectively, using a hydrothermal method. Surface charge, surface roughness, wettability, and fluoride release were measured for each coating. Surface chemistry was assessed using X-ray photoelectron spectroscopy and FA crystallinity using X-ray diffraction. Antibacterial activity against periodontopathogens was assessed in vitro using viable counts, confocal microscopy, and scanning electron microscopy (SEM). SEM showed that the hydrothermal method produced FA coatings that were predominately aligned perpendicular to the SS substrate or disordered FA coatings consisting of randomly aligned rodlike crystals. Both FA coatings significantly reduced the growth of all examined bacterial strains in comparison to the control. The FA coatings, especially the disordered ones, presented significantly lower charge, greater roughness, and higher area when compared to the control, enhancing bacteria–material interactions and therefore bacterial deactivation by fluoride ions. The ordered FA layer reduced not only bacterial viability but adhesion too. The ordered FA crystals produced as a potential novel implant coating showed significant antibacterial activity against bacteria implicated in peri-implantitis, which could be explained by a detailed understanding of their physicochemical properties.