The synthesis of porous silicon-based photonic structures for bio-sensing applications has been widely investigated in the last years. Thanks to its spongiform structure, porous silicon can efficiently host many organic molecules dispersed in solutions having proper chemical affinity. Fluorescent emission of organic-dyes embedded in porous silicon can be enhanced if a photonic structure like a Fabry–Pérot resonator is employed as a host solid matrix. In this work we present experimental evidence of a fluorescence enhancement effect obtained by means of doubly resonant microcavities tuned on both the excitation and the emission wavelengths. The use of doubly resonant cavities allows both a resonant excitation of dyes and a resonant amplification of the emission. We demonstrate that small concentrations of fluorescent dyes down to few picomoles can be detected. The bio-sensing capabilities of such a structure are tested on larger molecules of fluorescein-labelled protein A, yielding to an evident lowering of the detection limit by 2 orders of magnitude.