I begin the commentary by identifying some methodological challenges in interdisciplinary learning research and describe how the contributions to the special issue address these. The fact that interdisciplinary learning is collaborative, long-lasting, and distributed necessitates using rich data sources and mainly qualitative forms of analysis. The impossibility of experimental comparisons led the researchers to adopt an ecological perspective, focusing on multi-level causal pathways rather than linear cause-and-effect relationships. Furthermore, I propose establishing an “object commons” for sharing research on interdisciplinary learning, suggesting metadata standards like PROV for describing digital provenance. Reconstructing the provenance of (digital) knowledge objects resembles historical analysis. I therefore explore further how narratives can serve as scientific explanations, drawing parallels between narrative structures and graph-based provenance notation. I argue for the refinement of narrative formats using digital provenance methods to enhance systematic analysis and sharing of research findings. In conclusion, addressing the methodological challenges that are indigenous to research on interdisciplinary learning has the potential to advance the methodology arsenal of the Learning Sciences and of educational research more generally.