This paper reports a novel miniaturized pseudo reference electrode (RE) design for biasing Ion Sensitive Field Effect Transistors (ISFETs). It eliminates the need for post-CMOS processing and can scale up in numbers with the CMOS scaling. The presented design employs silane-mediated transfer of patterned gold electrode lines onto PDMS microfluidics such that the gold conformally coats the inside of microfluidic channel. Access to this electrode network is made possible by using “through-PDMS-vias” (TPV), which consist of high metal-coated SU-8 pillars manufactured by a novel process that employs a patterned positive resist layer as SU-8 adhesion depressor. When integrated with pneumatic valves, TPV and pseudo-RE network were able to bias 1.5 nanoliters (nL) of isolated electrolyte volumes. We present a detailed characterization of our pseudo-RE design demonstrating ISFET operation and its DC characterization. The stability of pseudo-RE is investigated by measuring open circuit potential (OCP) against a commercial Ag/AgCl reference electrode.