Background: In some areas of the world, breast milk is seen as a potential source of child diarrhoea. While this belief has been explored in African and Southeast Asian countries, it remains vastly understudied in Latin American contexts. We investigate socio-cultural factors contributing to breastfeeding cessation in rural high-altitude populations of the Peruvian Andes. The role of socio- cultural factors in the local explanatory model of child diarrhoea, and whether these perceptions were integrated in the local healthcare system were assessed. Methods: Within the framework of a randomised controlled trial, we conducted semi-structured interviews with 40 mothers and 15 health personnel from local healthcare centres involved in the trial. Results: Cultural beliefs on breastfeeding cessation included the perception that breast milk turned into “blood” after six months and that breastfeeding caused child diarrhoea. We identified eight local types of child diarrhoea, and women linked six of them with breastfeeding practices. “Infection” was the only diarrhoea mothers linked to hygiene and the germ disease concept and perceived as treatable through drug therapy. Women believed that other types of diarrhoea could not be treated within the formal healthcare sector. Interviews with health personnel revealed no protocol for, or consensus about, the integration of the local explanatory model of child diarrhoea in local healthcare and service provision. Conclusions: The local explanatory model in rural Andean Peru connected breastfeeding with child diarrhoeas. Cultural beliefs regarding diarrhoea management may increase home treatments, even in cases of severe diarrhoeal episodes. Future national breastfeeding support programmes should promote peer-counselling approaches to reduce negative attitudes towards breastfeeding and health practitioners. Local explanatory models should be incorporated into provincial and regional strategies for child diarrhoea management to promote equity in health and improve provider-patient relationships.