Despite the well-described abundance of phenol-degrading bacteria, knowledge concerning their degradation abilities under suboptimal conditions is still very limited and needs to be expanded. Therefore, this work aimed to study the growth and degradation potential of Stenotrophomonas maltophilia KB2 and Pseudomonas moorei KB4 strains toward phenol under suboptimal temperatures, pH, and salinity in connection with the activity of catechol dioxygenases, fatty acid profiling, and membrane permeability. The methodology used included: batch culture of bacteria in minimal medium supplemented with phenol (300 mg/L), isolating and measuring the activity of catechol 1,2- and 2,3-dioxygenases, calculating kinetic parameters, chromatographic analysis of fatty acid methyl esters (FAMEs) and determining the membrane permeability. It was established that the time of phenol utilisation by both strains under high temperatures (39 and 40 °C) proceeded 10 h; however, at the lowest temperature (10 °C), it was extended to 72 h. P. moorei KB4 was more sensitive to pH (6.5 and 8.5) than S. maltophilia KB2 and degraded phenol 5–6 h longer. Salinity also influenced the time of phenol removal. S. maltophilia KB2 degraded phenol in the presence of 2.5% NaCl within 28 h, while P. moorei KB4 during 72 h. The ability of bacteria to degrade phenol in suboptimal conditions was coupled with a relatively high activity of catechol 1,2- and/or 2,3-dioxygenases. FAME profiling and membrane permeability measurements indicated crucial alterations in bacterial membrane properties during phenol degradation leading predominantly to an increase in fatty acid saturation and membrane permeability. The obtained results offer hope for the potential use of both strains in environmental microbiology and biotechnology applications.