Clay-nanocomposite materials have been widely exploited as drug delivery systems, but their application in agriculture is less explored. In clay-nanocomposite, the combination of nanoclay and the active ingredient (i.e., metal, nonmetal, oxide nanoparticles) can produce a biocompatible and environmentally friendly delivery vehicle of micronutrients, pesticides, etc. for better crop growth. Clay-nanocomposites have been researched to address the problem of nontarget effects of agrochemicals, their leaching into groundwater, and the fast breakdown of sprayed chemicals. Here, we present a review of the synthesis of clay-based nanocomposites and their application as a delivery vehicle for agrochemicals and nucleic acids, as well as their antimicrobial properties. This review would be helpful in identifying and addressing the current issues of the delivery of active ingredients and biological macromolecules for crop protection, improved growth, and sustainability.