Differing worldviews give interdisciplinary work value. However, these same differences are the primary hurdle to productive communication between disciplines. Here, we argue that philosophical issues of metaphysics and epistemology subserve many of the differences in language, methods and motivation that plague interdisciplinary fields like educational neuroscience. Researchers attempting interdisciplinary work may be unaware that issues of philosophy are intimately tied to the way research is performed and evaluated in different fields. As such, a lack of explicit discussion about these assumptions leads to many conflicts in interdisciplinary work that masquerade as more superficial issues. To illustrate, we investigate how philosophical assumptions about the mind may influence researchers in educational neuroscience. The methods employed by researchers in this field are shaped by their metaphysical beliefs, and arguments around these issues can threaten accepted disciplinary ontologies. Additionally, how a researcher understands reduction in the special sciences and how they place their colleagues in this ontology constrains the scope of interdisciplinary projects. In encouraging researchers to explicitly discuss the philosophical assumptions underlying their research we hope to alleviate some of the conflict and establish realistic expectations for collaborative projects.