About 15 million people live in rural communities in the Russian Federation. Most of them are not energetically supplied from the main national infrastructures (electric and gas). People living in such isolated communities use diesel engines for generating electricity and heat. In many cases, diesel is supplied using rail tracks, boats or even helicopters. Consequently, the generation of electricity has very high costs and very low reliability. For this reason, more and more rural isolated communities are using renewable energy sources to decrease their dependency on diesel sources. This study deals with the concept of net-zero multi-energy systems in rural and stand-alone areas. A methodology, based on economical, ecological, technical and social criteria, has been developed for planning the generation capacity and sizing the energy storage units. In addition, controlling algorithms have been developed to deal with the volatility of renewable energy sources (wind and sun) and integrate heat/electricity energy systems. The proposed methodology has been applied to the design of a net-zero energy system for a Siberian rural energy community.