The purpose of this paper is to describe challenges in collaborative research in practice. The research object is a development process where a medium-sized and large manufacturer applied prototypes of a problem-solving practice on practical problems in product realization. These applications provided the manufacturers with insights into practical problems in product realization and their problem-solving capabilities. In addition, the application of the prototypes generated data for a case study about challenges in collaborative research. The findings reveal three challenges in collaborative research. The first challenges relates to scoping problems and action. The second challenge relates to practitioner’s immediate outcome from applying the problem-solving practice. The third challenge addresses practitioner’s commitment for change. Practitioners gained insight by applying prototypes; however, implications for practitioners emerge when mutual stakeholders have ambiguous or conflicting objectives for participating in research. Implications for research include tension between researchers and practitioners in the organization. Therefore, researchers, practitioners and consultants can benefit from considering these challenges when engaging in collaborative research.