Coffea arabica L. is as a tropical crop that can be grown under monocrop or agroforestry (AFS) systems, usually at altitudes greater than 600 m, with suitable environmental conditions to bean quality. This study aimed to assess the effect of altitude (650, 825, and 935 m) and light conditions (deep shade—DS, and moderate shade—MS provided by native trees, and full Sun—FS) on the physical and chemical attributes of green coffee beans produced in the Gorongosa Mountain. Regardless of altitude, light conditions (mainly MS and FS) scarcely affected most of the studied physical and chemical attributes. Among the few exceptions in physical attributes, bean mass tended to lower values under FS in all three altitudes, whereas bean density increased under FS at 650 m. As regards the chemical compound contents, sporadic changes were found. The rises in trigonelline (MS and FS at 935 m), soluble sugars (FS at 935 m), and the decline in p-coumaric acid (MS and FS at 825 m), may indicate an improved sensory profile, but the rise in FQAs (FS at 825 m) could have a negative impact. These results highlight a relevant uncertainty of the quality changes of the obtained bean. Altitude (from 650 to 935 m) extended the fruit maturation period by four weeks, and altered a larger number of bean attributes. Among physical traits, the average sieve (consistent tendency), bean commercial homogeneity, mass, and density increased at 935 m, whereas the bean became less yellowish and brighter at 825 and 935 m (b*, C* colour attributes), pointing to good bean trade quality, usually as compared with beans from 650 m. Furthermore, at 935 m trigonelline and 5-CQA (MS and FS) increased, whereas FQAs and diCQAs isomers declined (in all light conditions). Altogether, these changes likely contributed to improve the sensory cup quality. Caffeine and p-coumaric acid showed mostly inconsistent variations. Overall, light conditions (FS, MS, or DS) did not greatly and consistently altered bean physical and chemical attributes, whereas altitude (likely associated with lower temperature, greater water availability (rainfall/fog), and extended maturation period) was a major driver for bean changes and improved quality.
