At the earliest stage of pedogenesis, microorganisms are the main biological drivers of nutrient transformation and mobilization from rock minerals. However, this driving process is not yet well understood despite its importance for the formation and fertility of soil. The aim of this study was to determine the microbial accumulation of organic phosphorus (Po) and microbial release of bioavailable phosphorus (bio-P) from rock minerals and to analyse which factors control these processes. We hypothesized that microorganisms contribute to stabilization and accumulation of Po. For this purpose, we carried out a series of incubation experiments with model soils (with soil Po removed) and soil extracts of natural soil from the earliest stage of pedogenesis in the newest retreat area of the Hailuogou glacier. A modified Hedley fractionation method was used to characterize the P forms in soils. Microbial synthesis of Po was clearly observed in this study. In view of the fact that carbon (C) and nitrogen (N) are the main energy and material sources of microorganisms and that their stoichiometry plays an important role in microbial metabolism, we hypothesized that the C and N (ratio and level) play a regulatory role in microbial transformation of P. Therefore, the different C/N gradients were constructed in our incubation experiments. Results showed addition of C and N resulted in an accumulation of stable Po and decrease in pH in soils. These results suggest that not all microbial biomass P is easily degraded. Along two C/N ratio gradients (same ratio but keeping C vs N constant), opposite patterns of total Po (TPo) changes was observed. Opposite patterns were also observed for bio-P along the two C/N ratio gradients. Regardless of the C/ N ratio, high CN additions always led to lower TPo accumulations, higher bio-P releases and higher phosphatase activity compared to low CN additions. We conclude that microbial synthesis of Po contributed to the P fractions in soil stable residual pools and that microbial release of bioavailable P was driven by two modes (i.e., N-driven mode and C-driven mode). Our study highlights that microorganisms drive the accumulation of soil Po during the earliest stage of pedogenesis in our study area.