The detection of gravitational waves from extreme-mass-ratio inspirals with upcoming space-borne detectors will allow for unprecedented tests of general relativity in the strong-field regime. Aside from assessing whether black holes are unequivocally described by the Kerr metric, such detections may place constraints on the degree of spacetime symmetry. In particular, depending on exactly how a hypothetical departure from the Kerr metric manifests, the Carter symmetry, which implies the integrability of the geodesic equations, may be broken. Here, we examine the gravitational waveforms associated with non-integrable extreme-mass-ratio inspirals involving a small-mass companion and a supermassive compact object of general relativity, namely the Manko-Novikov spacetime. We show that the waveforms displays sudden frequency jumps, when the companion transverses resonant islands. These findings demonstrate that such abrupt manifestations in the gravitational-wave frequencies are generic, have a genuine astrophysical origin and function as a distinctive signature of chaotic phenomena in extreme-mass-ratio binaries.