Microbial communities are important determinants of ecosystem functions in deserts. However, bacterial communities and their relationship with edaphic conditions are poorly investigated in these extreme ecosystems. Here we examined the community structure and biomass of bacteria, including nitrogen-fixing bacteria, across different soil habitats in Qatar, using high-throughput sequencing and soil fatty acid profiling. To study bacterial community structure correlations and its edaphic drivers, we determined soil physicochemical parameters. Soils in the studied habitats were predominantly colonized by members of Proteobacteria, Actinobacteria, and Chloroflexi, while nitrogen-fixing bacteria were sparse, and the proportion of unidentified fungal taxa was relatively high. According to biomass estimates, there were more bacteria in soils of shrub- and woodlands in the Qatar Peninsula. This was mediated by the high concentration of gram-positive bacterial fatty acid biomarkers, whereas gram-negative bacterial biomarkers were more abundant in habitats with the highest salinity. Salinity also appeared to alter the community composition of bacteria as well as their diversity. Overall, soil phosphorus (P) concentration was positively correlated with the increase in diversity and biomass of bacteria and exhibited a pronounced effect on the community composition. These findings suggest P affects bacterial communities in various ways in these hot arid desert soils.