Soil protists, a diverse group of unicellular eukaryotic microorganisms, play a crucial role in soil ecosystems by regulating microbial populations, enhancing nutrient cycling, and contributing to soil fertility. As microbial predators, they facilitate organic matter decomposition, improve carbon sequestration, and interact with plant roots to promote growth, and their predatory activity suppresses soil-borne plant pathogens, thereby fostering disease-resistant agroecosystems. Beyond their ecological functions, protists serve as bio-indicators of soil health, responding to environmental changes, land use practices, and fertilization regimes. Recent advances in molecular techniques have expanded our understanding of protist diversity and function. However, research on soil protists remains limited, and their potential applications in sustainable agriculture are underexplored. This review examines the diversity, functional roles, and agricultural benefits of soil protists, focusing on their contributions to nutrient availability, plant-microbe interactions, and disease suppression. The recent methodological advancements, research challenges, and future perspectives for integrating protists into soil management strategies is also highlighted in this review. Unlocking the potential of soil protists could provide innovative solutions for improving soil fertility, enhancing crop productivity, and mitigating environmental stressors, ultimately promoting more resilient and eco-friendly agricultural systems.