BACKGROUND: COVID-19 vaccination is a global priority. Latin American countries have some of the highest COVID-19 death rates worldwide with vaccination hampered by a variety of reasons, including mis- and disinformation, vaccine hesitancy, and vaccine supply constraints. Addressing vaccine hesitancy through effective messages has been found to help increase vaccine uptake. Participatory processes could be used to co-design health messages for this purpose. OBJECTIVE: This article describes the methodology used to co-design evidence-based audio messages to be deployed in a cohort of individuals through an interactive voice response (IVR) mobile phone survey intervention, aimed towards increasing vaccination uptake in an adult population in Colombia. METHODS: Participants of the COVID-19 vaccination message co-design process included a sample of the general population of the country, representatives of the funder organisation, and research team members. The co-design process consisted of four phases: (1) formative quantitative and qualitative research, (2) message drafting based on the results of the formative research, (3) message content evaluation, and (4) evaluation of the voices to deliver the audio messages; and was informed by reflexive meetings. RESULTS: Three categories of evidence-based audio messages were co-designed, each corresponding to an arm of the mHealth intervention: (1) factual messages, (2) narrative messages, and (3) mixed messages. An additional fourth arm with no message was proposed for control. The iterative co-design process ended with a total of 14 audio messages recorded to be deployed via the intervention. CONCLUSIONS: Co-developing health messages in response to health emergencies is possible. Adopting more context-relevant, participatory, people-centred, and reflexive multidisciplinary approaches could help develop solutions that are more responsive to the needs of populations and public health priorities. Investing resources in message co-design is deemed to have a greater potential for influencing behaviours and improving health outcomes