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Mauritius has a long tradition of using cogeneration systems for electricity generation. Bagasse, a by-product of sugar cane is burnt in high temperature and pressure boilers to produce superheated steam to be used for combined heat and power generation. Steam is fed in condensing extraction steam turbine coupled with an alternator to produce electricity and the exit low pressure steam of the turbine is used for the processing of sugar with flexibility to be employed also in distillery and refinery activities. Multi-criteria analysis of such bio-refinery inputs and outputs is conducted considering Energy, Engineering, Economic, Environmental and Ethical dimensions like sustainability, equity and democratization of the energy sector. Due to the reduction of price obtained for the sale of sugar to the European Union, the sugar industry has to re-engineer itself to move towards the flexi-factory concept for its survival. Production of high value-added refined sugar/special sugars, dehydrated ethanol for transport and power use and green electricity are constrained by a host of factors from climatic conditions to the price of sugar on the world market through the grid power costs itself dependent on world oil and coal prices. Environmental standards are also to be considered. The aim of this paper is to optimize the cogenerated energy systems of the cane flexi-factory by a holistic energy systems analysis. Actual parameters of a flexi-factory are used to calculate the energy efficiency of each components parts of the system as well as social, economic and environmental benefits. Policy implications crucial to the future viability of such complex energy systems; these are fully discussed in relation to national and international objectives. [ABSTRACT FROM AUTHOR]