Including sustainability criteria for making decisions in project management poses challenges in the areas of bioenergy, biotherapeutics, and biomaterials. This is mainly due to chemical heterogeneity of bio-based materials, techno-economic feasibility, and triple constraint of time, cost, and product quality. However, bio-based technologies create opportunities as sustainable processes because they involve upvaluation of locally available renewable and biodegradable materials. This work was conducted to identify challenges and opportunities in incorporating project management tools in bioproduct development with the goal of integrating measurable sustainability criteria scores in decision-making. The scores or metrics from these tools can be used by project managers for decision-making in engineering process scale-up, evaluation of social impact, and commercialization of processing technologies.