Quantum sensors typically translate external fields into a periodic response whose frequency is then determined by analyses performed in Fourier space. This allows for a linear inference of the parameters that characterize external signals. In practice, however, quantum sensors are able to detect fields only in a narrow range of amplitudes and frequencies. A departure from this range, as well as the presence of significant noise sources and short detection times, lead to a loss of the linear relationship between the response of the sensor and the target field, thus limiting the working regime of the sensor. Here we address these challenges by means of a Bayesian inference approach that is tolerant to strong deviations from desired periodic responses of the sensor and is able to provide reliable estimates even with a very limited number of measurements. We demonstrate our method for an 171Yb+ trapped-ion quantum sensor but stress the general applicability of this approach to different systems.