A cost-effective label-free optical biosensor based on gold-coated self-ordered nanoporous anodic alumina bilayers is presented. The structure is formed by two uniform nanoporous layers of different porosity (i.e., a top layer with large pores and a bottom layer with smaller pores). Each layer presents uniform pore size, regular pore distribution, and regular diameter along its pore length. To increase and improve the output sensing signals, a thin gold layer on the top surface was deposited. The gold layer increases the refractive index contrast between the nanoporous alumina layer and the analytical aqueous solution, and it results in a greater contrast in the interferometric spectrum and a higher sensitivity of the structure. From this structurally engineered architecture, the resulting reflectivity spectrum shows a complex series of Fabry-Pérot interference fringes, which was analyzed by the reflective interferometric Fourier transform spectroscopy (RIFTS) method. To determine the performance of this structure for biosensing applications, we tested bovine serum albumin (BSA) as the target protein. The results show a significant enhancement of the RIFTS peak intensity and position when a gold layer is on the top surface.