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Coatings offer a means to control nanoparticle (NP) size, regulate dissolution, and mitigate runoff when added to crops through soil. Simultaneously, coatings can enhance particle binding to plants and provide an additional source of nutrients, making them a valuable component to existing nanoparticle delivery systems. Here, the surface functionalization of metal and metal-oxide nanoparticles to inhibit aggregation and preserve smaller agglomerate sizes for enhanced transport to the rooting zone and improved uptake in plants is reviewed. Coatings are classified by type and by their efficacy to mitigate agglomeration in soils with variable pH, ionic concentration, and natural organic matter profiles. Varying degrees of success have been reported using a range of different polymers, biomolecules, and inorganic surface coatings. Advances in zwitterionic coatings show the best results for maintaining nanoparticle stability in solutions even under high salinity and temperature conditions, whereas coating by the soil component humic acid may show additional benefits such as promoting dissolution and enhancing bioavailability in soils. Pre-tuning of NP surface properties through exposure to select natural organic matter, microbial products, and other biopolymers may yield more cost-effective nonagglomerating metal/metal-oxide NPs for soil applications in agriculture.