Participatory research is gaining popularity worldwide. However, there is a need of comprehensive metrics for assessing, monitoring, and guiding participatory research projects. In this study, we aimed to identify in the literature a set of multifaceted indicators that could be useful for evaluating participatory research projects in terms of sustainability. We then tested these indicators using as a case study a participatory biodiversity research project that is currently underway in Mexico. We selected 64 indicators, distributed among 11 categories, that we deemed potentially informative about the process, impact, and success of public involvement in the study of biodiversity. This set of indicators covered several aspects of socioecological systems, including environmental education, society, empowerment, economy, communication, biological conservation, and public policy. Through the assessment of the case study, we provide an example for (a) selecting, rating, and validating the identified set of indicators; and (b) generating information about the temporal trends, achievements, and actions needed to support this particular project. Our study provides valuable instruments for evaluating, comparing, managing, improving, and replicating participatory science initiatives (e.g., community-based projects, citizen science programs, participatory action research projects). The indicators that we propose could also function as policy tools to guiding funding decisions in a field that is rapidly gaining popularity across the globe. A comprehensive examination of participatory research projects could lead to better understanding, performance, and support of public inclusion in science.