Increasingly, plantations for food, fiber and wood, are necessary to provide a growing world population. Agroforestry systems become more and more important, however these systems usually develop in marginal conditions, limited land, restricted funding, occasional technical support and above this, there is limited documentation and evaluation of innovated traditional systems in indigenous and small-scale contexts, which challenge forest scientists. The aim of this research was to assess the quality of trees in plots managed by Mayan indigenous farmers who planted agroforestry systems with fine wood species to increase the value of land and labor in localities with highly-marginal social conditions in Northern Chiapas, México. Twenty oldest plots were selected within a group of previously established plots (eight with improved fallow, six with shaded coffee and six with maize crop associated to trees) where forest inventories were carried out in nested 100 and 1000 m2-circular plots. In all plots tree diameter, height, quality indicators and the incidence of the pest Hypsipyla grandella were measured. Trees in the maize-associated- to-trees system are favored by the practices applied to annual crop during the first 3rd–5th years, a period in which they are free from the interference of other trees and benefit from favorable light conditions, weeding and a higher intensive care from the farmer while shaded coffee and improved fallow have higher tree densities and a more closed canopy condition than maize associated to trees. In consequence, maize associated to trees shows 68.1 % stems with good form; shaded coffee and improved fallow averaged 40.5 and 39.7 % of good quality stems, respectively; improved fallow exhibited a greater number of suppressed trees thanshaded coffee and maize associated to trees (p\0.0001). In addition, maize associated to trees showed the highest proportion of trees with commercial value with 56.9 %, followed by improved fallow with 28.2 %, and shaded coffee with 11.8 % (p\0.0001); the rest were trees with domestic uses. However, maize associated to trees significantly result with high incidence of H. grandella probably due to the crown exposure. Timber volume averaged 92.9 ± 68.9 m3 for improved fallow, 77.3 ± 24.8 m3 for shaded coffee, and 52.5 ± 39.7 m3 for maize associated to trees. The value of the fine wood represents increment in income, variety of products and self-employment for households. Nonetheless, improved fallow and coffee plantations might benefit from the elimination of competitors from larger trees to favor promising immature ones and pruning, while maize crop associated to trees might benefit from opportune pruning for controlling the stem borer as well as tree replacement to achieve long term replacement and harvesting.