This paper presents a systemic intervention approach as a means to overcome the methodological challenges involved in research into computer-supported collaborative learning applied to the promotion of mathematical problem-solving (CSCL-MPS) skills in schools. These challenges include how to develop an integrated analysis of several aspects of the learning process; and how to reflect on learning purposes, the context of application and participants' identities. The focus of systemic intervention is on processes for thinking through whose views and what issues and values should be considered pertinent in an analysis. Systemic intervention also advocates mixing methods from different traditions to address the purposes of multiple stakeholders. Consequently, a design for CSCL-MPS research is presented that includes several methods. This methodological design is used to analyse and reflect upon both a CSCL-MPS project with Colombian schools, and the identities of the participants in that project. Copyright © 2013 John Wiley & Sons, Ltd.