Aroma and fragrance compounds have broad applications in the food, cosmetic and pharmaceutical industries. However, these compounds are mainly produced by chemical synthesis. An alternative, sustainable and promising route for the natural production of flavour compounds is microbial transformation processes. In this work, we obtained the production of different aroma compounds in significant concentrations, such as isoamyl acetate, isoamyl alcohol, ethyl acetate and acetaldehyde, among others, from agribusiness by-products (sugarcane molasses) and using Pichia fermentans. These were subsequently concentrated by pervaporation and microencapsulation by spray drying using different encapsulating agents. The results showed that when these techniques were applied to two iced beverages, they produced an odour of fruity notes, especially those of banana. In addition, woody and alcoholic notes were identified by the panellists. Finally, the best encapsulating agents were dextrin (73.49 ppm) and the dextrin and maltodextrin mixture (72.58 ppm