Salinity is one of the most important factors that limit the productivity of agricultural soils. Certain plant growth-promoting bacteria (PGPB) have the ability to stimulate the growth of crop plants even under salt stress. In the present study, we analysed the potential of PGPB Bacillus toyonensis COPE52 to improve the growth of tomato plants and its capacity to modify its membrane lipid and fatty acid composition under salt stress. Thus, strain COPE52 increased the relative amount of branched chain fatty acids (15:0i and 16:1 increment 9) and accumulation of an unknown membrane lipid, while phosphatidylethanolamine (PE) levels decreased during growth with 100 and 200 mM NaCl. Importantly, direct and indirect plant growth-promoting (PGP) mechanisms of B. toyonensis COPE52, such as indole-3-acetic acid (IAA), protease activity, biofilm formation, and antifungal activity against Botrytis cinerea, remained unchanged in the presence of NaCl in vitro, compared to controls without salt. In a greenhouse experiment, tomato plants (Lycopersicon esculentum 'Saladette') showed increased shoot and root length, higher dry biomass, and chlorophyll content when inoculated with B. toyonensis COPE52 at 0 and 100 mM NaCl. In summary, these results indicate that Bacillus toyonensis COPE52 can modify cell membrane lipid components as a potential protecting mechanism to maintain PGP traits under saline-soil conditions.