Collaboration is required between researchers, biodiversity managers, local businesses, government and indigenous communities to achieve conservation in most tropical regions. However, these different actors can function on different timescales, leading to asynchrony of goals, impeding partnership efforts and limiting the capacity of academic endeavours to fairly represent the diverse ontologies and perspectives. We reflect here on our experience of an on-going collaborative research programme around the Calakmul Biosphere Reserve, Mexico. Our research addressed biodiversity conflicts over jaguar by analysing relevant local social relations. The intention was to collaborate with local actors to ensure that research processes catalysed mutual learning, and findings were both accepted and useful. However, since we initiated the research (albeit with 20 years’ experience in the region) rather than local request for our input, collaboration had to be fostered. Firstly, we broadly explored people's environmental concerns to understand how jaguar conservation was perceived by local actors. We sought common ground to facilitate collaboration and listened to local issues. These discussions revealed the poor reputation of the scheme that compensated local farmers for livestock depredation by jaguar and we reported this to the administering committee. Secondly, we further evaluated local actors’ experiences of this compensation scheme and undertook workshops to improve it, together with a local conservation NGO and the Biosphere Reserve. Thirdly, we explored feelings of injustice regarding conservation. Overall, this research programme encouraged long-term engagement between local and international researchers and many local actors. It led to the co-design and implementation of a training workshop on conflict management. Despite excellent scholarship, the development of sound relationships, and eventual practical impacts, challenges were encountered. Local actors did not always want to engage with ‘our’ researcher agenda or were distracted e.g. by elections. Some partners did not fulfil prior stated commitments. Local ranchers, whilst friendly, expressed frustration at the lack of tangible short-term benefits. Six years later, the fruits of our persistence are visible: our academic outputs on jaguar conservation are requested by local initiatives and we co-wrote two proposals for practical projects. Our reflections illustrate how the pursuit of common ground and conservation embedded in justice are required to navigate collaborations and reduce our own bias. Despite the urgency of the biodiversity crisis, we need to be willing to listen to different voices, to be patient, and to recognise the different priorities and timescales of others for long-term understanding, action and transformation through transdisciplinary research.