The aim of this thesis was to assess the social-ecological factors that have shaped land-use change (historically) and smallholder land-use decisions (currently) in two neighboring villages in the Marqués de Comillas agro-forest frontier region, embedded in the Lacandona Rainforest, southern Mexico. The studied villages share some similarities but also exhibit differences regarding their land-use types and composition. This thesis was grounded on an empirical comparative case study. A mix-methods approach was used which consisted on qualitative (ethnographic work, oral histories, semi-structured interviews, farm visits, Photovoice method, among others) and quantitative (land-use change analysis using remote sensing, soils data and statistical modelling) methods. In general, land-use change analysis focuses on the study of the social dimension, often neglecting the biophysical one. Thus, this PhD research is important because it analyzes land-use change from an interdisciplinary lens, by addressing biophysical and social drivers of land-use change and smallholder decisions in the tropics.