In addition to improving coffee quality, producing coffee under various shade tree species is essential for maintaining and reviving agroecology and nature-based agroforestry techniques. The study was carried out in Ethiopia’s Oromia regional states in the Jimma Zone’s Chora Botor district (Chalalaki coffee plantation). The experiment was overlaid on coffee farm that has been established by using four released Arabica coffee varieties (7440,744, F59, and 75227) under three suggested coffee shade trees (Albizia gummifera, Millettia feruginea, and Acacia abyssinica). To evaluate the effect of shade tree species and coffee varieties on quality of coffee data on raw, organoleptic and biochemical traits were collected and analyzed using split plot design with three replications. The study’s findings demonstrated that, hundred bean weight (HBW) was only influenced by coffee varieties but not by shade tree species. On the other hand, coffee varieties and shade tree species had a substantial impact on raw quality (primary and secondary defects apart from odor), organoleptic quality (cup cleanness, acidity, body and flavor) and biochemical quality (caffein, total chlorogenic acid and trigonelline). Acacia abyssinica, and Albizia gummifera, are prominent shade tree species that improve the quality of coffee due to its contribution in soil organic matter build up through litter fall and, root decomposition, and slowdown of the rate of ripening of coffee cherries. This enhanced the development of beneficial compounds that improve the raw, organoleptic and biochemical qualities of coffee. The delayed ripening process of coffee under shade lead to higher quality coffee beans with desirable flavor Hence, choosing the right combination of coffee varieties and shade tree species is very crucial for improving coffee bean quality and sustainable production of coffee in coffee-based farming system of southwest Ethiopia.