An ecological challenge is to understand the effects of body size reduction in response to climate change, a phenomenon that could significantly disrupt agroecological systems. However, the effects of these changes in individual traits and trophic interactions on the structure of food webs in such systems have not yet been fully explored. In the Southern Hemisphere, the socioeconomic and cultural importance of agriculture justifies the need to investigate these systems. In this study, the selected host plant is watermelon (Citrullus lanatus), the pest corresponds to the cotton aphid (Aphis gossypii), and the potential biological control agent is the Chilean predatory mite (Eriopis chilensis). To theoretically understand the structure of this food chain, we developed a three-level model that includes biological control, two pests, and the host plant. The model combines a continuous dynamic system with discrete pulses representing births and the introduction of new individuals of the control agent. Holling’s type II functional responses, reproduction and mortality rates, and carrying capacity dependent on the body size of the species are integrated into the model. Additionally, a computational algorithm is presented, which enables the simulation of the behaviour of the agroecological system. This proposal offers a theoretical tool to improve the understanding of species interactions and to anticipate dynamics that could be useful in designing agroecological management and control strategies.