The tension between a growing global demand for food, rising environmental impacts of agricultural intensification, and the uncertainty of future changes in our global climate highlight a crucial need for sustainable alternatives to maintain and increase agricultural productivity. Microalgae are renewable resources with a broad range of options for applications in agricultural settings. This review examines how microalgae-based fertilizers improve soil properties and crop resilience. Microalgae enhance soil organic matter and phosphorus availability. They stabilize soil aggregates and increase water retention. Microalgae modify rhizosphere microbial diversity and boost nutrient cycling. Most studies are limited to short-term laboratory conditions, ignoring dynamic field stresses that inhibit microalgal functions. Key knowledge gaps exist in understanding microalgae-crop molecular interactions and biofilm metabolism in root environments. Future research should prioritize developing cost-effective cultivation techniques, advancing in-situ field monitoring, and screening regionally adaptive strains. Integrating microalgae into soil-microbe synergy frameworks is essential to unlock their potential as a cornerstone of sustainable agriculture, providing theoretical support for applications in diverse soil and climatic regions.