Currently, many agro-ecosystems are contaminated with toxic, hazardous compounds which can be broadly categorized as (a) anthropocentrically introduced xenobiotic agrochemicals (e.g., pesticides, insecticides, and fungicides), (b) secondary metabolites produced as a result of plant-microbe interactions, and (c) heavy metals which are mainly introduced through natural and anthropogenic processes. Organophosphates (OP), carbamates, pyrethroids, and neonicotinoids are among the most dominant groups of xenobiotic agrochemicals reported globally. These are highly toxic to non-target organisms including humans and many have been banned by the US Environmental Protection Agency or the European Union. Among these, neonicotinoids were introduced recently (in the 1990s), being comparatively less toxic to non-target higher vertebrates and most extensively used (149 crops in 120 countries). An example of a naturally produced hazardous compound is Deoxynivalenol (vomitoxin, DON), which is a highly toxic secondary metabolite (mycotoxin) produced by the mold Fusarium while infecting staple crops. Finally, Pb, Cr, Cd, As, Zn, Cu, and Fe are commonly encountered heavy metals in agroecosystems globally.