Here, continued development of cellulosic-based biofuels is needed to provide renewable energy and strengthen rural investment and development in the United States (US). To ensure biofuel development is sustainable and does not negatively affect ecosystem services, stakeholder input is necessary to identify sensitive and meaningful indicators. A major challenge is that there are substantial differences in terminology, perspectives, and methods used to quantify sustainability and ecosystem services with regard to processes, biodiversity, and socioeconomic effects. Our objectives were to identify relevant indicator categories for both perspectives using a case study from the US state of Iowa. A scientific literature review and engagement with stakeholders were used to identify 11 indicator categories associated with production, harvest, storage, and transport of cellulosic feedstocks. Five categories focus on environmental concerns (soil quality, water quality and quantity, greenhouse gas emissions, biodiversity, and productivity) and six on socioeconomic concerns (social wellbeing, energy security, external trade, profitability, resource conservation, and social acceptability). Although these indicators reflect sustainability concerns of these stakeholders, additional monitoring and stakeholder engagement are needed to support the continual improvement that is part of adaptive management.