Due to the constant growth of the human population and anthropological activity, it has become necessary to use sustainable and affordable technologies that satisfy the current and future demand for agricultural products. Since the nutrients available to plants in the soil are limited and the need to increase the yields of the crops is desirable, the use of chemical (inorganic or NPK) fertilizers has been widespread over the last decades, causing a nutrient shortage due to their misuse and exploitation, and because of the uncontrolled use of these products, there has been a latent environmental and health problem globally. For this reason, green biotechnology based on the use of microalgae biomass is proposed as a sustainable alternative for development and use as soil improvers for crop cultivation and phytoremediation. This review explores the long-term risks of using chemical fertilizers for both human health (cancer and hypoxia) and the environment (eutrophication and erosion), as well as the potential of microalgae biomass to substitute current fertilizer using different treatments on the biomass and their application methods for the implementation on the soil; additionally, the biomass can be a source of carbon mitigation and wastewater treatment in agro-industrial processes.