Nanoporous microbead-based microfluidic systems for biosensing applications allow enhanced sensitivities, while being low cost and amenable for miniaturization. The regeneration of the microfluidic biosensing system results in a further decrease in costs while the integration of on-chip signal transduction enhances portability. Here, we present a regenerable bead-based microfluidic device, with integrated thin-film photodiodes, for real-time monitoring of molecular recognition between a target DNA and complementary DNA (cDNA). High-sensitivity assay cycles could be performed without significant loss of probe DNA density and activity, demonstrating the potential for reusability, portability and reproducibility of the system.