Fluoride is the anionic form of fluorine, the 13th most abundant element in Earth's crust, and it is toxic to many organisms above a threshold concentration. Environmental bacteria can withstand relatively high fluoride concentrations, but the only mechanism described so far is the CrcB-dependent efflux. CrcB-mediated export is the primary mechanism of F-tolerance in the model environmental bacterium Pseudomonas putida, yet spontaneous NaF-tolerant mutants arise in the absence of the CrcB transporter, showing that this is not the sole pathway of tolerance. We used whole-genome sequencing, proteomic, and transcriptomic analyses to identify mechanisms that affect fluoride tolerance in Pseudomonas putida.