Product selection in the dynamic enzymatic synthesis of cyclodextrins can be controlled by changing the pH. Using cyclodextrin glucanotransferase to make labile the glycosidic linkages in cyclodextrins (CDs), we generate a dynamic combinatorial library of interconverting linear and cyclic α-1,4-glucans. Templates can be employed to favour the selective production of specific CDs and, herein, we show that by using ionisable templates, the synthesis of α-CD or β-CD can be favoured by simply changing the pH. Using 4-nitrophenol as the template, β-CD is the preferred product at low pH, while α-CD is the preferred product at high pH. Furthermore, a new methodology is described for the simulation of product distributions in dynamic combinatorial libraries with ionisable templates at any given pH.