Bioflavors and oligosaccharides are two classes of substances that may be produced biotechnologically through microbial bioprocesses. These compounds have attracted the interest of pharmaceutical and food industries not only due to their technological properties (sweetening/fiber or flavoring, respectively), but also as a consequence of other functional properties such as, for example, health promoting benefits. The use of agro-industrial residues as substrates in biotechnological processes seems to be a valuable alternative in helping to overcome the high manufacturing costs of industrial fermentations. This manuscript reviews the most important advances in biotechnological production of bioflavors and oligosaccharides. The use of some agro-industrial residues in such processes is also cited and discussed, showing that this is a rising trend in biotechnology.