A comprehensive examination of the physical and cup quality of Kafa Biosphere Reserve coffees was essential to identify the inherent qualities of the coffees in connection with the area’s soil physical and chemical characteristics. As a result, preliminary coffee quality data was acquired from bean physical and cup quality examination of coffees derived through a three-stage nested design combining districts (Gimbo, Gawata, and Decha), coffee production systems (forest, semiforest, and garden), and coffee processing methods (wet, semiwet, and dry). Representative soil samples were collected according to the sampling structure and analyzed following the standard procedures. Multiple factor analysis and Pearson’s correlation coefficient analysis were applied to the collected data. According to the results of multiple factor analysis, the Gimbo and Decha districts are not significantly different from each other in terms of coffee quality. However, they are substantially different from the Gawata district in terms of coffee quality. Similarly, within each district, there are no clear differences in coffee production systems. However, the production systems of districts varied significantly. The coffee processing method had a pronounced effect on the overall quality and preliminary grade, physical and raw quality variables of coffee. Screen retention (14) was correlated with soil iron, but it was related negatively to boron and sodium contents. A significant and positive relationship was observed between green coffee bean moisture content and soil potassium, calcium, magnesium, boron, sodium, organic carbon, silicon content, and soil pH. A positive and significant relationship between soil molybdenum and the coffee quality variable was observed across the studied districts whereas most soil micronutrients, specifically, zinc, sulfur, and manganese, were significantly and negatively related to the organoleptic qualities of the coffees. Further investigation that includes the effects of elevation is recommended in future studies.