A method and system for disinfecting and disinfesting a commodity, such as a perishable agricultural commodity, by treatment with an environment of low oxygen/high ballast gas with cycled pressure changes that overwhelm and damage the respiratory system of the insect without damaging the host commodity. The system and method may also include the introduction of disinfectants, antiseptics and other toxic chemicals or the exposure to radio frequencies with intense electric fields that may increase the metabolic activity of the pest or decrease the fitness of the pest within the low oxygen environment. Treatments according to the methods can also increase the shelf life of agricultural commodities by eradicating or delaying the growth of bacteria, fungi, protozoa and other microbial pests.