Highly sensitive dual-mode labeled detection of biotin in well-characterized porous silicon (PSi) films using colloidal quantum dots (QDs) as signal amplifiers are demonstrated. Optimization of the PSi platform for targeted QD infiltration and immobilization is carried out by characterizing and tuning the porosity, film depth, and pore size. Binding events of target QD-biotin conjugates with streptavidin probes immobilized on the pore walls are monitored by reflective interferometric spectroscopy and fluorescence measurements. QD labeling of the target biotin molecules enables detection based on a distinct fluorescent signal as well as a greater than 5-fold enhancement in the measured spectral reflectance fringe shift and a nearly three order of magnitude improvement in the detection limit for only 6% surface area coverage of QDs inside the porous matrix. Utilizing the QD signal amplifiers, an exceptional biotin detection limit of ≈6 fg mm−2 is demonstrated with sub-fg mm−2 detection limits achievable.