The increase in demand for continuous and real-time monitoring of permeation of biomolecules is addressed by using highly selective ultrathin silicon nanoporous membranes (SNMs) combined with detection using ultraviolet absorption. The membranes, with an average pore size of 8.8 nm, are fabricated using semiconductor batch processes including chemical vapor deposition and rapid thermal annealing. Bovine serum albumin (BSA) of a concentration of 250 μg/ml is used as the test molecule. The concentration of BSA diffused through the membrane is measured using optical transduction based in-house developed sensor. The photocurrent obtained from the sensor is measured every 15 min and compared with the standard Bradford assay at the same time-stamp. The concentration estimated by the sensor is found to agree with the Bradford assay with a standard deviation of 1.4%. The throughput of the membrane is increased by fabricating an array of SNMs, which showed an increase in diffusion rate by 3.8 times with respect to the single SNM. The clogging of pores by the biomolecules is analyzed using ionic conductivity experiments. The structural integrity of BSA diffused through the SNM is also analyzed. © 2019 IEEE.