Nowadays, coffee quality is the most appreciated characteristic in the international coffee trade. Different investigations have shown how various factors influenced the physical, organoleptic and biochemical characteristics of coffee; among these factors, altitude, shade, coffee variety, productivity (fruit load) and processing are the most important ones. Nevertheless, very few studies have been undertaken on more than two of these factors simultaneously. With the objective of evaluating the interactive effects of altitude, shade, yield and fertilization on coffee quality, 67 coffee samples were collected on coffee plantations in the Northern Central Region of Nicaragua. Altitude had the strongest influence on coffee physical characteristics, biochemical composition and organoleptic quality. Shade influenced significantly the physical characteristics and biochemical composition of coffee beans; nonetheless, the organoleptic quality was significantly enhanced by shade only in the altitudinal range of 950-1255 m. Fertilization and yield influenced positively physical characteristics of the coffee beans as well as their biochemical composition. The organoleptic quality was influenced by fertilization, but not by yield. Biochemical compounds showed strong relationships with organoleptic characteristics.