The isolation of cellulose nanocrystals (CNCs) by organic acid hydrolysis can contribute to reducing the extensive use of mineral acids, but aspects related to performance, cost effectiveness, and sustainability still need to be addressed. Here, techno-economic analysis (TEA) and life cycle assessment (LCA) were performed to evaluate the production of CNCs using organic and/or inorganic acid hydrolysis, in the context of a sugar cane biorefinery. CNCs were extracted from sugar cane bagasse using sulfuric acid (S-CNC), citric acid (Cit-CNC), and their combination (Cit-S-CNC). The nanodimensional structures were highly dependent on the type of acid used, but all the conditions resulted in nanostructures with CNC characteristics. The minimum product selling price values calculated by TEA for Cit-CNC and Cit-S-CNC were 34.0% and 37.2% higher, respectively, compared to S-CNC, mainly due to the high cost of citric acid recovery. The citric acid hydrolysis and recovery steps had substantial environmental impacts, accounting for up to ∼58% of the gobal warming potential values for Cit-CNC and Cit-S-CNC, which were more than 2fold higher than for S-CNC. These findings showed the importance of using TEA and LCA tools to support decision making in the selection of nanocellulose isolation routes in future biorefineries.