In forests, intraspecific genetic variation in trees can affect the entire ecosystem, which in turn, depends on the different processes occurring through space and time in soil. We hypothesized that, in addition to the effect of the local site, tree genotype and season would have an effect on the properties and functions of the edaphic environment. We studied soils beneath different genotypes of Pinus pinaster Ait. (Atlantic, Mediterranean and African) in 45‐year old common gardens in spring and autumn. The pH, organic matter, nutrients and infrared spectroscopy together with enzyme activities were determined and used to evaluate the soil properties and biogeochemical functioning. In addition to strong site effects, tree genotype and seasonal effects were detected on soil properties and functions. Both were major controlling factors of microbially mediated functioning, especially processes related to the carbon (C) and nitrogen (N) cycles. In general, the soil environment beneath the Atlantic trees was different from that under the Mediterranean and African genotypes, with differences in raw infrared spectra and increased activities of enzymes involved in hemicellulose degradation and N mobilization. Regarding the season, the largest soil humidity (RH), electric conductivity (EC), and N and potassium (K) concentrations, coupled with the smallest phosphorus (P) concentration and C:N ratios were detected in autumn. Degradation of C peaked in autumn, while P and N mobilization usually peaked in spring. Our results showed that, beyond local site effects, there were detectable effects of tree genotype and season in Mediterranean forest soils, which governed microbially mediated processes that might have relevant functional consequences at the ecosystem level.