HES (hybrid energy system)s are becoming energy systems of choice for standalone applications due to ever increasing fuel costs and global concern on GHG (Green House Gas) emissions. However, it is difficult to justify the higher ICC (Initial Capital Cost) of renewable energy components, especially for rural electrification projects in developing countries. This paper illustrates the modeling and simulation of HESs, and multi-objective optimization carried out in order to support decision-making in such instances. LEC (Levelized Energy Cost), ICC and GHG emission were taken as objective functions in the optimization and the sensitivity of market prices and power supply reliability was further evaluated. Results depict that Pareto front of LEC, ICC and GHG emission can be simplified as a combination of ICC–LEC and LEC–GHG emission Pareto fronts making the decision-making process simpler. Gradual integration of renewable energy sources in a number of design stages is proposed for instances where it is difficult to bear the higher ICC. Finally, importance of planning integration of renewable energy sources at early design stages of the project is highlighted in order to overcome the difficulties that need to be faced when coming up with the optimum design. •Multi-objective optimization considering LEC (Levelized Energy Cost), ICC (Initial Capital Cost) and GHG (Green House Gas) emission.•3-D Pareto front can be simplified as a combination of two 2-D Pareto fronts.•Sensitivity of the fuel price is notable in LEC–ICC Pareto front.•Gradual integration of renewable energy sources is suggested in order to bear higher ICC.