In this paper, the design and the characterization of a novel interrogator based on integrated Fourier transform (FT) spectroscopy is presented. To the best of our knowledge, this is the first integrated FT spectrometer used for the interrogation of photonic sensors. It consists of a planar spatial heterodyne spectrometer, which is implemented using an array of Mach-Zehnder interferometers (MZIs) with different optical path differences. Each MZI employs a 3_3 multi-mode interferometer, allowing the retrieval of the complex Fourier coefficients. We derive a system of non-linear equations whose solution, which is obtained numerically from Newton's method, gives the modulation of the sensor's resonances as a function of time. By taking one of the sensors as a reference, to which no external excitation is applied and its temperature is kept constant, about 92% of the thermal induced phase drift of the integrated MZIs has been compensated. The minimum modulation amplitude that is obtained experimentally is 400 fm, which is more than two orders of magnitude smaller than the FT spectrometer resolution.