Refrigeration is vital in fresh-produce supply chains for minimizing food losses. However, it requires energy and impacts the environment. To optimize the control and logistics of postharvest cold chains, we need to better identify trade-offs between maintaining fruit quality and reducing environmental impacts. Therefore, we propose a novel computational method, by combining life cycle assessment with virtual cold chains. This holistic approach allows us, on the one hand, to track the thermal history of the cooling process and fruit quality decay of each single fruit in an entire pallet throughout the cold chain, using computational fluid dynamics. On the other hand, the carbon footprint of the supply chain is quantified. This pioneering method enriches life cycle assessment with more customized input data from multiphysics modeling, and at the same time assesses food quality evolution throughout the supply chain. Significant differences between ventilated carton designs (63 g CO₂-eq/kg) and cold chain scenarios (11 g CO₂-eq/kg) were identified, namely, 10% and 1.6% of the environmental impact of the entire supply chain, respectively. If solar electricity is used for precooling, the environmental impact was reduced by 55 g CO₂-eq/kg of fruit (or 8.5%), while still providing similar fruit quality retention. By combining climate impact with the predicted quality retention, this method will help retailers to choose the most optimal package design and cold chain scenario to make their food supply chains more sustainable. This approach can be applied as well to life cycle assessment of biogas conversion of food waste, amongst others.