In this work, we propose a spectral interferometric technique for detecting the wavelength position of the resonances of low-cost optical resonators, consisting in rectangular glass microcapillaries. Moreover, we exploited these microdevices as core elements of a microoptofluidic sensing platform designed for the measurements of the refractive index (RI) of fluid samples, based on spectral phase shift interferometry. A detailed theoretical model was implemented to simulate the spectral shape of the interferometric signal in a wavelength range where cavity resonances of the capillary-based optical resonator occur. For experimental verification, the microdevice was placed at the end of the measurement arm of a Michelson interferometer and illuminated using a light source emitting broadband radiation in the near infrared region around 1.55 μm. The resonances of the empty capillary (i.e., filled with air) were successfully detected as steep phase jumps of the interferometric cosine signal recorded as a function of the wavelength, in good agreement with the theoretical predictions. Finally, further experimental measurements were carried out by filling the capillary channel with water-glucose dilutions with different concentrations to prove the suitability of the phase shift detection method to monitor RI variations with respect to a reference fluid.