Traditionally, biological barriers are assessed in vitro by measuring trans-endothelial/epithelial electrical resistance (TEER) across a monolayer using handheld chopstick electrodes. Implementation of TEER into organ-on-chip (OOC) setups is a challenge however, due to non-uniform current distribution and interference from biomaterials typically found in such systems. In this work, we address the pitfalls of standard TEER measurement through the application of porous membrane electrical cell-substrate impedance sensing (PM-ECIS) to an OOC setup. Gold leaf electrodes (working electrode diameters = 250, 500, 750 µm) were incorporated onto porous membranes and combined with biocompatible tape to assemble microfluidic devices. PM-ECIS resistance at 4 kHz was not influenced by presence of collagen hydrogel in bottom channels, compared to TEER measurements in same devices, which showed a difference of 1723 ± 381.8 Ω (p=0.006) between control and hydrogel conditions. A proof of concept, multi-day co-culture model of the blood-brain barrier was also demonstrated in these devices. PM-ECIS measurements were robust to fluid shear (5 dyn/cm2) in cell-free devices, yet were highly sensitive to flow-induced changes in an endothelial barrier model. Initiation of perfusion (0.06 dyn/cm2) in HUVEC-seeded devices corresponded to significant decreases in impedance at 40 kHz (p<0.01 for 750 and 500 µm electrodes) and resistance at 4 kHz (p<0.05 for all electrode sizes) relative to static control cultures, with minimum values reached at 6.5 to 9.5 hours after induction of flow. Our microfluidic PM-ECIS platform enables sensitive, non-invasive, real-time measurements of barrier function in setups integrating critical OOC features like 3D co-culture, biomaterials and shear stress.