Controlled fermentation processes have high potential for improving coffee quality. The effect of fermentation temperature on beverage quality was investigated with coffee cultivated at elevations between 1166 and 1928 m. A completely randomized design was carried out at five elevation ranges at 200 m intervals in five farms per elevation range, and two temperatures (15 °C and 30 °C), which were maintained in a temperature-controlled bioreactor. Each temperature-controlled fermentation batch had a spontaneous fermentation batch (control treatment). Microbial identification of LAB and yeast was performed using a Biolog™ MicroStation™ ID System, and cup quality tests were performed following the SCA protocol. Tests conducted at 15 °C showed higher microbial community activity on the substrates used, indicating greater transformation potential than those conducted at 30 °C or those of spontaneous fermentation. According to Wilcoxon and Kruskal–Wallis tests, temperature-controlled fermentation resulted in high-quality coffee for all elevation ranges, with coffee from higher elevations and processed at controlled temperatures of 15 °C receiving the highest cup scores compared to coffee that was subjected to 30 °C. These results suggest that controlled temperature can be used to design standardized fermentation processes in order to enhance coffee quality through differentiated sensory profiles.