Crop production has a large impact on the nitrogen (N) cycle, with consequences to climate, environment, and public health. Designing better N management will require indicators that accurately reflect the complexities of N cycling and provide biological meaning. Nitrogen use efficiency (NUE) is an established metric used to benchmark N management. There are numerous approaches to calculate NUE, but it is difficult to find an authoritative resource that collates the various NUE indices and systematically identifies their assets and shortcomings. Furthermore, there is reason to question the usefulness of many traditional NUE formulations, and to consider factors to improve the conceptualization of NUE for future use. As a resource for agricultural researchers and students, here we present a comprehensive list of NUE indices and discuss their functions, strengths, and limitations. We also suggest several factors—which are currently ignored in traditional NUE indices—that will improve the conceptualization of NUE, such as: accounting for a wider range of soil N forms, considering how plants mediate their response to the soil N status, including the below-ground/root N pools, capturing the synchrony between available N and plant N demand, blending agronomic performance with ecosystem functioning, and affirming the biological meaning of NUE.