In Peru, nearly half of children aged 6–36 months were diagnosed with anaemia in 2017. To address this disease, the Peruvian Ministry of Health implemented a national programme in 2014, distributing free micronutrient powders (MNPs) to all children of this age. However, rates of childhood anaemia remain high. The aim of this study was to explore factors at all levels of the Social-Ecological Model that affect MNP use and adherence in Arequipa, an Andean city with childhood anaemia rates higher than the national average. We conducted in-depth interviews with 20 health personnel and 24 caregivers and 12 focus group discussions with 105 caregivers. We identified numerous barriers, including negative side effects (constipation, vomiting, and diarrhoea), poor taste of MNP, lack of familial and peer support for its use, insufficient informational resources provided by the health system, and limited human resources that constricted health personnel abilities to implement MNP programming successfully. Facilitators identified included concern about the long-term effects of anaemia, support from organizations external to the health system, well-coordinated care within the health system, and provision of resources by the Ministry of Health. We found that community or organizational and societal factors were key to limited MNP use and adherence, specifically the limited time health personnel have to address caregivers' doubts during appointments and the lack of informational resources outside of these appointments. Potential policy implications could be to increase informational resources available outside of individualized counselling by strengthening existing collaborations with community organizations, increasing media coverage, and providing group counselling.