Abstract Background A major challenge for clinical supervisors is to encourage their residents to be independent without jeopardising patient safety. Residents’ preferences according to level of training on this regard have not been completely explored. This study has sought to investigate which teaching methods of the Cognitive Apprenticeship (CA) model junior, intermediate and senior residents preferred and why, and how these preferences differed between groups. Methods We invited 301 residents of all residency programmes of Javeriana University, Bogotá, Colombia, to participate. Each resident was asked to complete a Maastricht Clinical Teaching Questionnaire (MCTQ), which, being based on the teaching methods of CA, asked residents to rate the importance to their learning of each teaching method and to indicate which of these they preferred the most and why. Results A total of 215 residents (71 %) completed the questionnaire. All concurred that all CA teaching methods were important or very important to their learning, regardless of their level of training. However, the reasons for their preferences clearly differed between groups: junior and intermediate residents preferred teaching methods that were more supervisor-directed, such as modelling and coaching, whereas senior residents preferred teaching methods that were more resident-directed, such as exploration and articulation. Conclusions The results indicate that clinical supervision (CS) should accommodate to residents’ varying degrees of development by attuning the configuration of CA teaching methods to each level of residency training. This configuration should initially vest more power in the supervisor, and gradually let the resident take charge, without ever discontinuing CS.