This work presents a methodology for integrating bio-energy supply chain networks with combined heat and power generation networks and heat demand of industrial processes. The industrial heat demand profile investigated involves multiple periods of operations and multiple utilities in heat exchanger networks requiring retrofit. The approach adopted involves a 3-layered superstructure, with the first layer comprising the bio-energy supply chain network that provides energy sources for steam generation. The second layer comprises the energy generation hub, where the bio-energy feedstocks of the first layer are converted to heat and power. A portion of the high-pressure steam generated in the energy hub layer and the intermediate steam levels exiting the turbines are fed to the third layer as hot utilities to satisfy the hot utility demand of the multi-period heat exchanger network. The multi-period network, which is to be simultaneously retrofitted and optimised with the networks of the first and second layers of the integrated superstructure, is also fed with steam generated from fossil sources in the second layer. The overall superstructure is modelled as a multi-objective mixed integer non-linear program considering economics and environmental impact as objectives. The solution obtained for the integrated model involves the selection of certain quantities of feedstocks from all available feedstocks supply locations. The retrofitted multi-period network competes favourably in terms of investment cost with solutions of existing methods, and it uses a mix of the available renewable and non-renewable energy sources.