The effect of arabica coffee management intensity on composition, structure and regeneration of moist evergreen Afromontane forests was studied in three traditional coffee management systems of Southwest Ethiopia: semi-plantation coffee (SPC), semi-forest coffee (SFC) and forest coffee (FC). Vegetation and environmental data were collected in 84 plots from forests varying in intensity of coffee management. After controlling for environmental variation (altitude, aspect, slope, soil nutrient availability and soil depth), differences in woody species composition, forest structure and regeneration potential among management systems were compared using one way ANOVA. The study revealed that intensification of forest coffee cultivation to maximize coffee production negatively affects diversity and structure of Ethiopian moist evergreen Afromontane forests. Intensification of coffee productivity starts with the conversion of forest coffee to semi-forest coffee, with significant negative effects on tree seedling abundance. Further intensification leads to the conversion of semi-forest to semi-plantation coffee, causing significant diversity losses and the collapse of forest structure (decline of stem density, basal area, crown closure, crown cover and dominant tree height). Our study underlines the need for shade certification schemes to include variables other than canopy cover, and that the loss of species diversity in intensively managed coffee systems may jeopardize the sustainability of coffee production itself through reduction of ecosystem resilience and disruption of ecosystem services related to coffee yield, such as pollination and pest control.