An essential aspect to the assessment process was to start with clear rules for participants and a conceptual framework that balanced legitimacy (participatory open process not influenced by politics), credibility (participation of renowned specialists and traceable primary data) and relevance (provides updated and non-prescriptive relevant information for the solution of problems). NCM was inspired by the Millennium Ecosystem Assessment but had to be adapted to the particular circumstances and characteristics of Mexico, one of the most biologically and culturally diverse countries.

Several challenges were faced, many of which arose because the authors worked pro-bono and had limited time. Firstly, deadline extensions were common as volume editors, authors and peer reviewers struggled with the initial deadlines. Secondly, many authors did not adhere to format specifications or some were changed to meet the demands of the editor team. Thirdly, there was a heavy workload for a small secretariat, which increased delays in delivering chapters to the editorial teams. Fourthly, data was dispersed in different sources and there was a lack of integrated data information sources (with the exception of the biodiversity data in the National Information System on Biodiversity).