<p>Adoption of green technologies is essential for the transition to cleaner industrial systems. To stimulate green technology adoption, decision makers (DMs) will need to consider several design criteria&#xa0;while targeting for the best performance. A significant challenge in the green technology adoption is the hesitancies of DMs. Uncertainty in a technology’s performance is among the factors affecting hesitancies. However, focusing solely on the&#xa0;uncertainties will hamper opportunities of future performance satisfactory. An interplay between indeterminacy and potential performance, therefore, exists in the adoption of green technologies. The optimum balance between the two is needed. DMs will need to determine this balance when integrating green technologies in industry system designs. To resolve this, this study presents a neutrosophic linear programming (NeLP) model in the design of an industry system given the indeterminacies of green technologies. This study uses notions of membership, non-membership, and indeterminacy of neutrosophic sets for degrees of satisfaction, dissatisfaction, and indeterminacy of relevant stakeholders. Risk tolerances of the stakeholders are based on each process’ technology readiness levels (TRLs). The model is tested in a case study of a biorefinery system where the results demonstrated changes in system design performance when indeterminacy is considered. In the case study, the system’s profit reduced by 16% under a neutrosophic environment. This study provides a methodological approach in assisting DMs when designing cleaner industry systems given the indeterminacies of green technologies.</p> Graphical abstract <p></p>