We investigate the transition to synchronization in ensembles of coupled oscillators with quenched disorder. We find that small coupling is able to increase the frequency disorder and to induce a spread of oscillator frequencies. This new effect of anomalous desynchronization is studied with numerical and analytical means in a large class of systems including Rössler, Lotka–Volterra, Landau–Stuart, and Van-der-Pol oscillators. We show that anomalous effects arise due to an interplay between nonisochronicity and natural frequency of each oscillator and can either increase or inhibit synchronization in the ensemble. This provides a novel possibility to control the synchronization transition in nonidentical systems by suitably distributing the disorder among system parameters. We conjecture that our results are of relevance for biological systems.