There are limited approaches available that enable researchers and practitioners to conduct multiple case study comparisons of complex cases of collaboration in natural resource management and conservation. The absence of such tools is felt despite the fact that over the past several years a great deal of literature has reviewed the state of the science regarding collaboration. Much of this work is based on case studies of collaboration and highlights the importance of contextual variables, further complicating efforts to compare outcomes across case-study areas and the likely failure of approaches based on one size fits all generalizations. We expand on the standard overview of the field by identifying some of the challenges associated with managing complex systems with multiple resources, multiple stakeholder groups with diverse knowledges/understandings, and multiple objectives across multiple scales, i.e., multifaceted collaborative initiatives. We then elucidate how a realist methodology, within a critical realist framing, can support efforts to compare multiple case studies of such multifaceted initiatives. The methodology we propose considers the importance and impact of context for the origins, purpose, and success of multifaceted collaborative natural resource management and conservation initiatives in social-ecological systems.