The steadily increasing global popularity of Greek strained yoghurt has necessitated alternative valorization approaches for acid whey, the major straining process effluent. In this context, prebiotic galacto-oligosaccharides can be enzymatically synthesized from acid whey lactose, via either commercial or novel β-galactosidases. A comparative study of galacto-oligosaccharide production from acid whey was carried out, employing two commercial β-galactosidases (from Kluyveromyces lactis and Aspergillus oryzae) and one novel, in-house produced (from Thermothielavioides terrestris), as a function of the initial lactose content and enzyme load. Selected reaction conditions for β-galactosidases from K. lactis, A. oryzae, and T. terrestris were 35 °C at pH 7.2, 45 °C at pH 4.5, and 50 °C at pH 4.0, respectively. Maximum galacto-oligosaccharide yields equal to 23.7, 23.4, and 25.7% were achieved with, respectively, 0.13 U/mL of K. lactis β-galactosidase in non-concentrated acid whey, 4 U/mL of A. oryzae β-galactosidase, and 8 U/mL of T. terrestris β-galactosidase in acid whey concentrated to 20% w/v initial lactose content. The increased galacto-oligosaccharide productivity of the thermophilic β-galactosidase from T. terrestris can be a determining asset in a combined concentration and oligomerization industrial process. This will allow for high galacto-oligosaccharide yields for efficient, cost-effective production of valuable prebiotics from acid whey.