Southeast Asia is a region that produces high amounts of key food commodities and includes areas of divergent socio-economic status. Food security is a high-priority issue for sustainable global development both quantitatively and qualitatively. In recent decades, adverse effects of unexpected contaminants on crop quality have threatened both food security and human health. Public concern about the adverse environmental and human health impacts of organochlorine contaminants led to strict regulations on their use in developed nations two decades ago. Nevertheless, DDT and several other organochlorine insecticides are still being used for agriculture and public health programs in developing countries in Asia and the South Pacific. As a consequence, humans in this region are exposed to greater dietary levels of organochlorines. Heavy metals and metalloids (e.g., Hg, As, Pb, Cd, and Cr) can jeopardize human metabolomics, contributing to morbidity and even mortality. Those during crop production include soil nutrient depletion, water depletion, soil and water contamination, and pest resistance/outbreaks and the emergence of new pests and diseases.