This contribution presents the synthesis of sustainable larger-scale supply networks to produce alternative energy and bioproducts across an entire system’s lifetime. In particular, production of food, first, second and third generation of biofuels, hydrogen, and renewable electricity are considered. Corn and wheat grain are used for production of food; corn stover, wheat straw, miscanthus, forest residue, algae oil and waste cooking oil are biomass and waste sources for the manufacture of bioproducts; and solar, wind and geothermal sources for electricity production. The objective of supply network synthesis is the maximization of Sustainability Net Present Value, which is a sustainability metric composed of economic, environmental and social net present values. The dynamic mixed-integer linear programming problem is formulated as a multi-period model where i) monthly time periods are used for the manufacture of biomass and bioproducts, while ii) daily, hourly and monthly periods are used for the production of electricity. A case study of EU-27 is considered and gradual energy transition from the current energy supply to 100 % renewable-based production of fuels and electricity over a time horizon of 40 y is investigated. The results of this study indicate that long-term transition from fossil to renewable-based generation of electricity, fuels and bioproducts is possible to a large extent. The results suggest an optimal selection of types, locations and dynamics of technology installations across the EU in order to achieve energy transition in the transport and electricity sectors.