Objective To analyse the contribution of participatory action research (PAR) in designing and implementing joint training sessions as a means to improve clinical coordination in a public health care network in Bogotá, Colombia. Methods A qualitative, descriptive-interpretative study using semi-structured individual interviews and focus groups with 40 professionals (GPs, specialists, members of the local steering committee (LSC) and network middle managers) involved in designing and implementing joint training sessions to improve cross-level clinical coordination. The intervention consisted of two forms of joint training sessions for GPs and specialists, implemented through two PAR cycles. Results The PAR approach in designing and implementing joint training sessions led to greater awareness of clinical coordination problems and helped adapting sessions to the local health care context. Study participants highlighted the role of LSC leadership during the PAR process and the importance of ensuring the necessary resources for adopting the intervention. Limited institutional support and differences between joint training sessions affected doctors’ participation and reduced the time available to conduct the sessions. The use of a reflexive method was essential in enhancing doctors’ participation, along with session duration, the facilitator’s role and session content. Conclusions The study provides evidence regarding the contribution of a PAR process to designing and implementing joint training sessions for improving clinical coordination. The findings can inform similar approaches in other health systems.