Context: Learning goal programmes are often created to help students develop self-regulated learning skills; however, these programmes do not necessarily consider the social contexts surrounding learning goals or how they fit into daily educational practice. Objectives: We investigated a high-frequency learning goal programme in which students generated and shared weekly learning goals with their clinical teams in core Year 3 clerkships. Our study explores: (i) how learning goals were incorporated into the clinical work, and (ii) the factors that influenced the use of students’ learning goals in work-based learning. Methods: We conducted semi-structured interviews with 14 students and 14 supervisors (attending physicians and residents) sampled from all participating core clerkships. Interviews were coded for emerging themes. Using cultural historical activity theory and knotworking as theoretical lenses, we developed a model of the factors that influenced students’ learning goal usage in a work-based learning context. Results: Students and supervisors often faced the challenge of reconciling contradictions that arose when the desired outcomes of student skill development, grading and patient care were not aligned. Learning goals could function as tools for developing new ways of acting that overcame those contradictions by facilitating collaborative effort between students and their supervisors. However, for new collaborations to take place, both students and supervisors had to engage with the goals, and the necessary patients needed to be present. When any one part of the system did not converge around the learning goals, the impact of the learning goals programme was limited. Conclusions: Learning goals are potentially powerful tools to mediate interactions between students, supervisors and patients, and to reconcile contradictions in work-based learning environments. Learning goals provide a means to develop not only learners, but also learning systems.