Shade coffee farming has been promoted as a means for combining sustainable use of forests and biodiversity conservation. With the increasing intensification of coffee production, methods of habitat quality assessment using measuring body conditions of individual birds may provide a more direct evidence of the contemporary quality of shade coffee farming for avian biodiversity before any demographic changes can be noticed. With this study, we applied fluctuating asymmetry on tarsi length and ptilochronology (relative growth bar width) to determine the habitat quality of shade coffee farming. The extend of fluctuating asymmetry in tarsus length showed no difference between shade coffee farming and natural forest in any of the studied avian functional guilds (forest specialist and generalist, as well as obligate and opportunistic insectivores). Similarly, no difference was found in growth bar width in any of these guilds with the exception of forest specialist birds which had narrower growth bars in shade coffee farming than in natural forests. No early sign of negative effect of shade coffee habitat on avian communities was noticed in the Ethiopian shade coffee using the biomarkers except on the forest specialist birds which were already reported to be less abundant in shade coffee farming from demographic studies. Shade coffee farming benefit avian diversity. However, the promotion of shade coffee farming should emphasis the conversion of degraded forest to shade coffee farming plantation but not the conversion of natural forest to shade coffee farming habitat as it adversely affect forest specialist birds.