Healthcare coordination is considered key to improving care quality. Although participatory action research (PAR) has been used effectively to bridge the gap between evidence and practice in other areas, little is known about the key success factors of its use in healthcare organizations. This article analyses the factors influencing the implementation of PAR interventions to improve clinical coordination from the perspective of actors in public healthcare networks of Brazil, Chile, Colombia, Mexico and Uruguay. A qualitative, descriptive-interpretative study was conducted in each country's healthcare network. Focus groups and semi-structured individual interviews were conducted to a criterion sample of: local steering committee (LSC) (29), professional platform (PP) (28), health professionals (49) and managers (28). Thematic content analysis was conducted, segmented by country and themes. The PAR process led by the LSC covered the return of baseline results, selection of problems and interventions and design, implementation and adjustment of the intervention, with PP. Interventions were implemented to improve communication and clinical agreement between primary and secondary care. Results reveal that contextual factors, the PAR process and the intervention's content influenced their implementation, interacting across time. First, institutional support providing necessary resources, and professionals' and managers' willingness to participate, emerge as contextual pivotal factors, influenced by other factors related to: the system (alignment with policy and political cycle), networks (lack of time due to work overload and inadequate working conditions) and individuals (not knowing each other and mutual mistrust). Second, different characteristics of the PAR process have a bearing, in turn, on institutional support and professionals' motivation: participation, flexibility, consensual decision-making, the LSC's leadership and the facilitating role of researchers. Evidence is provided that implementation through an adequate PAR process can become a factor of motivation and cohesion that is crucial to the adoption of care coordination interventions, leading to better results when certain contextual factors converge. © The Author(s) 2020. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.