Land-use changes threaten biodiversity and ecosystem services. Some of the last remaining forest fragments in Ethiopia, and the world’s only habitats that retain genetically diverse wild Arabica coffee populations, have experienced rapid recent conversion to coffee farms, plantations and agricultural fields. We examined patterns of remnant woody plant diversity in the remaining forests, and assessed the potential and limitations of coffee agroforests to maintain this diversity. We explored patterns of woody biodiversity, structure, and regeneration in forest fragments and on adjacent smallholder and large-scale state-owned shade-coffee farms. A total of 155 native woody species including rare/threatened species of Baphia, Cordia, Manilkara, and Prunus were recorded. Of these species, 56 (36.2%) and 18 (12%) were restricted to forest fragments and coffee farms respectively. Smallholder and large-scale coffee farms maintained 59% and 26% of the 155 recorded native woody species compared to the 137 species (88%) found in forest fragments. Native woody species regeneration in state-owned plantations was lower than in smallholder farms, which in turn was lower than forest fragments. Coffee farms could support a considerable portion, though not all, of the woody biodiversity of disappearing forests. Persistence of forest woody diversity and associated ecosystem services depends strongly on the scale and type of shade coffee cultivation pursued.