Contemporary agriculture is characterized mainly by extensive fertilizer application. Worldwide, fertilizer application indeed contributes greatly to increase in crop yield, but it also causes several negative effects such as soil acidification, water eutrophication, greenhouse gas emission, and resource depletion, thereby threatening the sustainable development of agriculture. Soil microbes drive plant diversity and productivity in terrestrial ecosystems, and they are directly involved in regulating the ability of plants to acquire nutrients and the nutrient cycles occurring in soils. Therefore, it is feasible to reduce the dependence of agriculture on fertilizers through the development of soil microbial approaches. Here, we described the role of biological nitrogen fixation, mycorrhizal fungi, and plant growth-promoting rhizobacteria in enhancing the ability of plants to acquire nutrients, and the underlying mechanisms. Moreover, we investigated the effect of soil microbes on soil nitrogen and phosphorus cycles, and their relationship with soil nutrient bioavailability and nutrient loss. Based on the obtained information, soil microbial processes to improve plant nutrition have been suggested, with the objective of reducing fertilizer application. Numerous studies have demonstrated the vital role of soil microbes in improving plant nutrition, but many problems regarding the use of soil microbial approaches need to be solved. Further extensive research in this field will help us solve these problems, and accelerate the development and application of soil microbial techniques for reducing fertilizer use, thereby contributing to sustainable agriculture.