The replacement of traditional process design approach by a more holistic approach is exigent in view of developing sustainable industrial systems and effectively reducing the energy and emission intensities in the process industries. Polygeneration systems are flexible and integrated multi-product systems that can potentially enhance energy efficiency, minimise financial risk and mitigate environmental impact. This paper presents a systematic conceptual process design and decision-making framework for facilitating multi-criteria analysis and selection of design options by considering three major criteria at process level-energy, environment and economy (3E). In this framework, three major steps are carried out: (i) defining system boundary, (ii) performance evaluation on the inner and outer system boundaries, (iii) 3E performance evaluation. 3E metric is proposed and it is derived from the relative economic worthiness associated with process energy intensity, greenhouse gas intensity and energy recovery which collectively indicates the techno-economic and environmental performances of a system with respect to the base case system. The methodology has been demonstrated through methanol and electricity production system with eight alternative configurations. Among the configurations under consideration, high offgas recycle for methanol production followed by electricity generation in series configuration has been found to carry the best 3E performance. (C) 2015 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.