We review and analyze the possible advantages and disadvantages of plant-stress-related metabolic and structural changes on applications in the fruit and vegetable processing industry. Knowledge of the cellular and tissue transformations that result from environmental conditions or industrial manipulation is a powerful means for food engineers to gain a better understanding of biological systems in order to avoid potential side effects. Our aim is to provide an overview of the understanding and implementation of physiological and biochemical principles in the industrial processing of fruits and vegetables.