The preservation of perishable food via cold supply chain is essential to extend shelf life and ensure food safety. However, the use of refrigeration processes requires energy consumption with economic and environmental impact. Increasing the temperature set point in cold equipment could save energy, but the global cost may increase due to food waste or safety issues. The study of potentially conflicting objectives such as food safety, food waste, and energy consumption may be challenging because the comparison between the outcomes of those objectives (risk of illness, amount of food waste, energy consumption in kWh). Methodologies leading to overcome issues involving conflicting impacts and the knowledge of their limitations are essential to support decision makers. This study focuses on the modeling of the energy consumption of cold facilities, food temperature, food contamination and growth of Listeria monocytogenes and lactic acid bacteria in a puff pastry plant. An event based framework was used to model the main components of the production line (kneader, conveyor, cooling spiral and cold room). Own-checks (microbial and temperature) data from food industry premises were used to inform and parameterize the model. Different scenarios were tested to evaluate the impact of operating conditions (setting temperature and duration) on energy consumption, food waste and food safety. Results showed that the temperature setting of the cooling spiral had a low impact on energy consumption and a high impact on the microbial quality. The opposite phenomena were observed in the cold room with a moderate impact of the cold room temperature setting on the food microbial quality and a high impact on energy consumption. Finally, a multi-criteria decision analysis approach is proposed to identify the optimal operating conditions regarding the three criteria. Criteria weights were set by the operators of the food plant (quality manager, production manager, energy advisor and plant director). This methodology helps manufacturers in decision making to optimize operating conditions and reduce energy consumption with a limited impact on food waste and safety.