Third-party certification (TPC), the most common organic certification system, has faced growing criticism in recent years. This has led to the development of alternative certification systems, most of which can be classed as Participatory Guarantee Systems (PGS). PGS have been promoted as a more suitable, cheaper and less bureaucratic alternative to TPC for local markets and are associated with additional benefits such as empowering smallholder farmers, facilitating farmer-to-farmer learning and enhancing food security and sovereignty. PGS have spread rapidly in the past few years, but studies suggest that they are facing numerous challenges that, if not addressed, may jeopardise these benefits. Using the example of three Mexican PGS initiatives, this paper explores the main challenges faced by PGS, specifically those predominantly found in producer-run PGS initiatives. Based on producer and consumer surveys, semi-structured and informal interviews, and participant and non-participant observation, the key challenges that emerged were continuous implementation of the certification process, time constraints, personal conflicts and conflict avoidance. The paper further argues that the requirements for PGS recognition under the Mexican Law for Organic Products may also threaten the continued existence of PGS and suggests that mechanisms for managing conflicts, incentivising PGS participation and mitigating opportunity costs are key if PGS are to continue to develop.