In this paper we propose a goal programming model that provides a consensual aggregated solution minimizing conflicts to guide multi-stakeholder decision-making processes and generates information regarding stakeholder groups to be exploited for negotiation purposes. This model permits to quantify variations in conflicts when the relative contribution of each criteria changes and gives insight to negotiation strategies with application in conservation areas. A dataset of a case study in the Meseta Ibérica Biosphere Reserve (Portugal-Spain) was used to test and validate the model. Fifty people belonging to four groups (scientists, government, farmers and businesspersons) assessed 20 management objectives in four dimensions: conservation, logistical support, development, and governance. The results showed the highest conflicts to be found for fauna and flora, education, and guarantees objectives while the most conflictive groups were scientists and farmers. The proposed model substantially reduced the global and intergroup conflicts associated to the same objectives, modelling the weights assigned to each objective in each dimension to find the most consensual/least conflictive solutions. This model can be a useful tool to improve complex decision-making processes in conservation areas with strong conflicts between stakeholders, such as transboundary biosphere reserves.