Herein we report the use of tetrakis(guanidinium) pyrenetetrasulfonate (G4PYR) and bis(guanidinium) 1,5‐napthalene disulfonate (G2NDS) to catalyze the cyclization of 2‐cyanobenzamide (1) to isoindolone (2). Moreover, we demonstrate the remarkable selectivity of these guanidinium organosulfonate hosts in encapsulating 2 over 1. By thoroughly investigating the intramolecular cyclization reaction, we determined that guanidinium and the organosulfonate moiety acts as the catalyst in this process. Additionally, 2 is selectively encapsulated, even in mixtures of other structurally similar heterocycles like indole. Furthermore, the tautomeric state of 2 (amino isoindolone (2‐A) and imino isoindolinone forms (2‐I)) can be controlled by utilizing different guanidinium organosulfonate frameworks.