The excessive use of chemical fertilizers has generated serious environmental and health problems, including soil degradation, water pollution, and greenhouse gas emissions. Microalgae-based biofertilizers are emerging as sustainable alternatives due to their ability to provide essential nutrients and bioactive compounds, such as phytohormones and exopolysaccharides. This chapter reviews current evidence demonstrating that microalgal biomass improves soil fertility, stimulates microbial and enzymatic activity, and increases crop yields by 15–30% while maintaining low greenhouse gas emissions. Furthermore, studies show their role in soil regeneration, reducing nitrogen leaching, and contributing to the circular economy. In contrast, chemical fertilizers are linked to soil acidification, biodiversity loss, eutrophication, and health risks in exposed populations. The findings presented highlight the potential of microalgae to progressively replace chemical fertilizers, positioning them as strategic allies for sustainable agri-food systems.