The decarbonization of industrial energy systems which comprise different networks (such as steam, water, electric power, fuel sources) is crucial for mitigating climate change and achieving sustainability goals. This paper presents a comprehensive methodology integrated in an open-source in-house tool for the coupled design and operation optimization of energy systems in industrial settings. The proposed approach integrates advanced optimization techniques with modeling of energy systems including properties like mass flow and temperature to simultaneously optimize both design parameters and operational strategies. The methodology encompasses the optimized integration of various energy technologies, such as renewable energy technologies, energy storage, and power-to-heat technologies while considering changing operational conditions and variable energy demand and supply. A multi-objective optimization framework is employed to balance conflicting targets, such as minimizing greenhouse gas emissions, operational costs, and ensuring system reliability. The in-house tool application considering a case study based on a food industry process demonstrates the effectiveness of the proposed approach in significantly reducing carbon footprints as well as operational and investment costs compared to traditional low-fidelity methods incorporated in commercial tools. The optimized concept achieved through the in-house tool has shown 8.5% less emission (EMI) compared to the optimized designs of the commercial tool. It shows 36% reduction in CO2 emissions compared to the existing facility of the case study. The optimized energy concept can be implemented in the existing facility with a payback period of 4.6 years. The outcomes of the selected use-case highlight the importance of coordinated design and operation decisions in achieving optimal performance and sustainability in industrial energy systems. It also shows an ideal workflow for making optimized design decisions to decarbonize industry with novel energy concepts. Thus, this work provides a robust foundation for future research and practical applications aimed at accelerating the transition towards low-carbon industrial processes.