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In biosensing applications, the exploitation of organic transistors gated via a liquid electrolyte has increased in the last years thanks to their enormous advantages in terms of sensitivity, low cost and power consumption. However, a practical aspect limiting the use of these devices in real applications is the contamination of the organic material, which represents an obstacle for the realization of a portable sensing platform based on electrolyte-gated organic transistors (EGOTs). In this work, a novel contamination-free microfluidic platform allowing differential measurements is presented and validated through finite element modeling simulations. The proposed design allows the exposure of the sensing electrode without contaminating the EGOT device during the whole sensing tests protocol. Furthermore, the platform is exploited to perform the detection of bovine serum albumin (BSA) as a validation test for the introduced differential protocol, demonstrating the capability to detect BSA at 1 pM concentration. The lack of contamination and the differential measurements provided in this work can be the first steps towards the realization of a reliable EGOT-based portable sensing instrument.