<p>Agroforestry is generally seen as beneficial for biodiversity conservation in agricultural landscapes, but this may not always be the case. While coffee-based agroforestry is widely recognized for supporting biodiversity, the impact of traditional coffee farming on indigenous woody species composition and regeneration is still not well understood. This study examined the impact of traditional coffee farming on the composition and regeneration status of naturally growing woody species in the Abe Dongoro District, West Ethiopia. Woody species data were recorded and diameter at breast height was measured for all individuals of woody plants in 60 sample plots of 400 m² area (30 from semi forest coffee (hereafter called SFC) and 30 from the natural forest). Seedling and sapling density of woody plants was calculated from smaller sub-plots within the main plots. The study identified 79 woody species from 70 genera and 39 families, including 40 species found in the semi forest coffee. Euphorbiaceae and Fabaceae were the most predominant plant families. Moreover, there are significant differences in species richness, evenness, and stem density between natural forest and semi forest coffee (SFC), but diameter class distribution revealed an inverted J shape in both SFC and natural forest. Moreover, SFC exhibited poor regeneration, primarily due to intensive coffee farming practices, which negatively affected forest structure, natural regeneration, and species composition. Hence, the commonly held belief that states traditional coffee farming conserve biodiversity needs to be reevaluated. In addition, a combination of sustainable practices that balance productivity with ecosystem health should be promoted in both natural Forest and SFC.</p>