A framework for selecting and evaluating indicators of bioenergy sustainability is presented. This framework is designed to facilitate decision-making about which indicators are useful for assessing sustainability of bioenergy systems and supporting their deployment. Efforts to develop sustainability indicators in the United States and Europe are reviewed. The first steps of the framework for indicator selection are defining the sustainability goals and other goals for a bioenergy project or program, gaining an understanding of the context, and identifying the values of stakeholders. From the goals, context, and stakeholders, the objectives for analysis and criteria for indicator selection can be developed. The user of the framework identifies and ranks indicators, applies them in an assessment, and then evaluates their effectiveness, while identifying gaps that prevent goals from being met, assessing lessons learned, and moving toward best practices. The framework approach emphasizes that the selection of appropriate criteria and indicators is driven by the specific purpose of an analysis. Realistic goals and measures of bioenergy sustainability can be developed systematically with the help of the framework presented here.