We analyze the design process of EDUguia chatbot, which includes diverse evidence from questionnaires and workshops with students and lecturers, as well as intermediary design objects. Based on the qualitative analysis, we identify several challenges that are transversal to the co-design work, as well as specific to the design phases. We critically reflect on the strategies deployed to overcome these challenges and how they relate to decision-making processes, highlighting the need to make stakeholders’ tacit knowledge explicit, cultivate trust-building and support democratic decision-making in technology design processes. The recommendations we present in this paper contribute to developing best practices in the collaborative design of chatbots for the self-regulation of learning, as well as learning technology in general.