Design and implementation of more sustainable natural resource management systems is the current objective of many research institutions, development agencies, NGOs and other stakeholders. But, how to assess whether a system is sustainable? How do we know whether the alternatives designed will increase the sustainability of the system? How to evaluate or assess the sustainability of natural resource management systems? In this paper we present a multiscale methodological framework for sustainability evaluation. The framework is based on a systems approach from which five general attributes of sustainable natural resource management systems are defined based on scale- and discipline-independent properties (productivity, stability, resilience, reliability and adaptability). A general operational strategy to derive site-specific criteria and indicators for the attributes at different scales is also presented. This strategy is based on the definition of impact scales, at which the different stakeholders can or want to design alternatives, as well as the main stakeholders objectives and constraints. The application of the multiscale framework is illustrated with a case study in the Purhepecha Region of Michoacán, a peasant mountainous region in the west of Mexico. We used stakeholder consultation to identify the main objectives and constraints as well as to select criteria and indicators. The sets of criteria and indicators suggested for the different scales of analysis of the Purhepecha Region are comprehensive, yet not exhaustive, and represent the main issues related to natural resource management in the region. Further work will be directed towards the quantification of indicators at different scales and their relationships and trade-offs.