We study the quasinormal frequencies of three effective geometries of nonrotating regular black holes derived from loop quantum gravity. Concretely, we consider the Ashtekar-Olmedo-Singh and two Gambini-Olmedo-Pullin prescriptions. We compute the quasinormal frequencies of axial and polar perturbations adopting a WKB method. We show that they differ from those of classical general relativity and, more importantly, that isospectrality is broken. Nevertheless, these deviations are tiny, even for microscopic black holes, and they decay following an inverse power law of the size of the mass of the black holes. For the sake of completeness, we also analyze scalar and vector perturbations, reaching similar conclusions.