The rhizosphere is the soil that surrounds, and is influenced by, the roots of a plant. It is considered one of the most complex ecosystems on the planet due to the intense interactions that occur between plants and microorganisms, as well as the competition that occurs among the microbial components. Due to this competition and beneficial interactions, a contribution of paramount relevance occurs in terms of chemical, physical, and biological characteristics that allow the plant and crop development. To mitigate ecosystem disturbances, it is necessary to compensate the imbalance of these conditions. Unfortunately, human activities involving strong soil disturbance have significantly affected plant development. Therefore, currently it is a priority to avoid the deterioration of soil ecosystems to remediate the damages that have already occurred. In the case of soil microbiology area, there are many solutions that can be designed and applied with beneficial microorganisms, including both fungi and bacteria, that interact mutualistically with plants or crops. At the same time, a deep understanding of these interactions remains challenging due to their complexity. In this review, biotechnological developments with agricultural or forestry importance are analysed. These include plant growth promoter bacteria, the Azolla-Anabaena symbiotic system, arbuscular mycorrhizal fungi and ectomycorrhizal fungi, as well as their relevance in the production of agricultural and forestry biofertilizers.