The selections of product portfolios, processing routes and the combination of technologies to obtain a sustainable biorefinery design according to economic and environmental criteria represent a challenge to process engineering. The aim of this research is to generate a simple but yet robust methodology that assists the process engineers to understand the environmental and economic behaviour of biorefinery systems. The novel Economic Value and Environmental Impact analysis (EVEI) methodology is presented in this paper. EVEI analysis is a tool that emerges from the combination of the value analysis method for the evaluation of economic potential and environmental footprinting for impact analysis. A quick illustration of the methodology in providing insights into the performances of a process network is given by taking a bioethanol plant as case study. The applicability to analyse biorefinery systems for selection of process pathway alternatives is demonstrated by using a Jatropha-based biorefinery case study. The systematisation of the methodology allowed its implementation and integration into a Computer Aided Process Engineering (CAPE) tool in the well known Excel® environment using the built-in VBA facility. This will accelerate the design process allowing focus on the analysis of results and devising alternatives from highly complex integrated process schemes.