The growth of global population continuously increases the demands for agroforestry-derived products, underpinning a sustainable growth of energy matrix in the sectors of food security, transportation, and industrial is momentous. The high demand for the sustainable energy sources has led to an increase in the application of pesticides associated with growing crops for the production of biofuel. In 2019, the global consumption of pesticides was 4.2 million tonnes. Case studies on life cycle assessment (LCA) of pesticides showed that toxicity is the major severe impact of pesticide usage, contributing to human toxicity (∼70%) and freshwater eco-toxicity (>50%). This alarming situation needs a solution as conventional pesticides pose various negative impacts to human and the environment, rendering the biofuel production process unsustainable. In this review, we focus on the interaction between pesticide use, biofuel production, food security for a sustainable balancing in between government benefits, environmental, and human health, aiming to track the implications and impact to the global efforts towards achieving the UN Sustainable Development Goals (SDGs). Even though, there are strict government regulations and legislations pertaining to pesticide use, and policies devised as guidelines for agroforestry sectors to implement and monitor these measures, the discrepancies still exist in between national and supranational entities. To cater the above issue, many efforts have been made to upscale the biofuel production, for example, the United States, Brazil, China and Indonesia have ventured into biofuels production from non-food-crops based feedstock while other developing nations are rapidly catching up. In this perspective, a sustainable nexus between Biofuels-Pesticides-Agroforestry (BPA) is essential to create a sustainable roadmap toward the UN SDGs, to fulfilling the energy, food, and land security. The contribution of technologies in BPA includes genetic modified crops, integrated pest and weed management with controlled release pesticides, use of nano-biopesticides is being reviewed. As a whole, the concept of biofuel processing complex (BPC) and farmers upskilling, together with the effective implementation of efficient policies and Internet of Things (IoT) would be the key to drive the BPA nexus towards fulfilment of SDGs.