In this paper a two level hierarchical methodology is presented for the integral design of hybrid power generation systems based on alternative renewable energy (ARE) systems using the net energy concept and considering technical, economical, societal as well as environmental aspects. Results are presented for the design of a small-scale hybrid renewable energy system using the proposed methodology in Margarita Island, Venezuela. The proposed methodology applies the integrated analytical hierarchy process (AHP) methodology to the selection of the best hybrid renewable energy system using the concept of net energy and is divided in two phases: a classic optimization process using levelized costs minimization and an AHP implementation for decision making problems. Under this methodology technical–economical aspects are considered as quantitative parameters, while social–environmental aspects depend largely on the criteria of the system planning engineers and future users of the system. Technical–economical aspects are considered using specialized software, used to optimize and compute the best configuration of an ARE project. Social–economical aspects are defined as a series of parameters that should be considered by the planning team, a meeting of experts or a community consensus on the project site. Several diesel price scenarios (low, intermediate and high) are considered. The results show the importance of the proposed tools for decision making problems.