Despite the growing number of published studies on student learning in the laboratory, there is a critical need to improve methodological rigor. Resonating with discussions on research methods, this paper outlines the importance of theory-informed research questions, the minimization of researcher and participant biases, and the use of triangulation and iteration in data collection to establish rigor. An illustrative case is presented within the context of a large interdisciplinary research project aimed at improving laboratory learning at the university level. The project incorporates two research avenues: one focusing on literature and faculty perspectives, and the other on a comprehensive assessment of multidimensional learning in the laboratory. The project employs a mixed methods paradigm and is grounded in a conceptual framework that conceptualizes laboratory work as epistemic practice, requiring a holistic analysis of student learning. The article concludes by discussing the results and implications of the project's findings, which are synthesized to highlight aspects of establishing methodological rigor. The overarching goal is to develop a comprehensive assessment instrument that captures the complexity and richness of the laboratory learning environment. The findings from this research are expected to contribute to the advancement of laboratory education research by providing a model for methodological rigor that can be applied across various scientific and interdisciplinary contexts.