This paper presents a structured approach for the efficient operation of multi-carrier energy systems under the uncertainty of renewable energy sources. As the penetration of wind and solar energy increases, managing the resulting variability becomes critical to maintaining both economic efficiency and operational flexibility. To address this, a two-stage multi objective optimization framework is proposed. In the first stage, the objective is to minimize daily operational costs while incorporating the uncertain behavior of renewables using a scenario-based stochastic approach. The second stage focuses on simultaneously enhancing system flexibility by maximizing the available capacities for both electrical and thermal energy generation and improving green house emissions. To evaluate system adaptability, two performance indicators are introduced: the Average Energy Generation Flexibility Index (AEGFI) and the Average Thermal Generation Flexibility Index (ATGFI). The optimization model is solved using the Modified Water Evaporation algorithm. Sensitivity analyses are also conducted to explore the effects of fluctuations in gas and electricity prices on system performance. The proposed model is applied to a generalized multi-carrier energy system. Simulation results demonstrate significant improvements in flexibility, with AEGFI and ATGFI increasing by 27.43% and 39.91%, respectively. Overall, the framework offers a comprehensive solution to balance cost-effectiveness and flexibility in energy systems with high shares of renewables.