Microplastics (MPs) are now recognized as a pervasive and escalating threat to agricultural ecosystems. Intensive use of plastics in farming, combined with inputs such as organic fertilizers, sewage sludge, and wastewater, continuously introduces MPs into soils. Once present, these particles interfere with plant physiological and biochemical processes, impair growth, and disturb soil structure and function. A particularly critical concern is their disruption of nutrient availability, reducing nitrogen (N) and phosphorus (P) availability, and influencing the activity of key enzymes such as phosphatases, urease, and β-glucosidase, thereby hampering nutrient cycling and mineralization. In parallel, MPs reshape soil microbial communities, suppressing beneficial microbes, compounding nutrient imbalances, and decreasing fertility. These cascading disruptions threaten not only crop productivity and soil sustainability but also human health through food-chain transfer. This chapter critically examines the mechanisms by which MPs influence nutrient cycling and microbial functionality and discusses microbiome-based strategies as promising avenues to restore soil health and ensure sustainable agriculture.