Background: Drylands are areas under continuous degradation and desertification largely covered by cyanobacterial biocrusts. Several studies have already shown that soil microorganisms play a fundamental role in the correct soil functioning. Nevertheless, little is known about the relationship taxonomy-function in arid soils and, in particular, in cyanobacterial biocrusts. An in-depth study of the taxonomic composition and the functions carried out by soil microorganisms in biogeochemical cycles was here carried out by using a shotgun metagenomic approach. Results: Metagenomic analysis carried out in this study showed a high taxonomic and functional similarity in both incipient and mature cyanobacterial biocrusts types with a dominance of Proteobacteria, Actinobacteria and Cyanobacteria. The predominant functional categories related to soil biogeochemical cycles were “carbon metabolism” followed by “phosphorus, nitrogen, sulfur, potassium and iron metabolism”. Reads involved in the metabolism of carbohydrates and respiration were the most abundant functional classes. In the N cycle dominated “ammonia assimilation” and “Nitrate and nitrite ammonification”. The major taxonomic groups also seemed to drive phosphorus and potassium cycling by the production of organic acids and the presence of extracellular enzymes and specialised transporters. Sulfur assimilation was also predominantly led by actinobacteria via the acquisition of sulfur from organosulfonated compounds. The main strategy followed for iron uptake seemed to be the synthesis and release of siderophores, mostly derived from representatives of the genus Pseudomonas. Conclusions: The absence of significant differences between both type of biocrusts was suggested to be due to the identical habitat-specific characteristics, the inherent variability associated with metagenomic sampling and experimental design limitations. There is metabolic diversity of respiration processes over the photosynthesis, but a diverse group of microorganisms, predominantly Actinobacteria and Proteobacteria were also involved in CO2 fixation metabolism. A preferential uptake of ammonium over nitrate as an economic strategy to avoid the high consumption of ATP was confirmed. Moreover, the functional redundancy presented by the microbial community was interpreted as a strategy to maintain the correct functioning of the soil biogeochemical cycles and therefore of the ecosystem in general. Evidence of sythrophic growth was nevertheless observed. Biotechnological potential as plant growth promoters was also identified.