Activity theory is a relatively young methodology for researching higher education teaching practices. Beyond systemic analyse of workplace activities and their development, activity theory used in its full interventionist capacity can foster practitioners' transformative agency to initiate practice change. Nevertheless, this is not an easy process. This paper shares activity theory research into the digital teaching activity of anatomy teachers within an Australian university. Using the lens of this project, the paper exposes several methodological dilemmas experienced by the researcher. Beyond the issue of the methodological level of activity theory used, these dilemmas relate to the authentic determination of both the unit of analysis and the object of the activity, the type of intervention (i.e. full Change Laboratory or modified), and the complexity in analysis using a concept-rich theory. Sharing these dilemmas invites further research to examine inherent contradictions in the human activity of conducting activity theory research focussed on university teaching.