Shade-grown, montane coffee agroforestry systems have the potential to conserve native tree species of conservation concern (CC) and typical of old growth or late succession (LS) forests in montane cloud forests. However, it remains unclear how preferential selection by farmers for or against certain tree species and diameter sizes affects CC and LS trees distribution and abundance. To address this issue, we investigated how management practices may inadvertently compromise the potential of agroforestry systems to serve as reservoirs for CC and LS trees. We sampled tree diversity in 31 coffee farms and 10 forest sites in La Sepultura Biosphere Reserve in Chiapas, Mexico and assessed the relative importance of shade tree density, basal area, proportion of Inga spp. trees, previous land use, and age of fallow (for farms established on land with an agricultural history) on the proportions of CC and LS trees. We then examined if tree size distributions differed between farms and forests, and whether land use legacies mediated the impact of the explanatory variables of interest. These analyses found that management practices that sought to increase the proportion of Inga spp. trees had the largest negative impact on the proportions of trees of LS and CC, but the magnitude of the effects were dependent on land-use legacy. We also found that tree size distributions differed between farms and forests among smaller trees (5–20cm diameter at breast height, (DBH)), but not among larger trees (>30cm DBH). These findings suggest that in order to increase the conservation potential of coffee agroforestry systems, particularly for farms established on land with an agricultural history, it is important to promote farmers’ tolerance of tree species other than Inga spp. and preferred tree species.