Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities’ assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0–15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.