In recent years, poly(3,4-ethylenedioxythiophene): poly(styrenesulfonic acid) (PEDOT: PSS)-based organic electrochemical transistors (OECTs) have been intensively studied, and various applications have been explored, such as neural interfaces, cell electrophysiological recording and wearable electronics. Furthermore, PEDOT: PSS OECTs have gained attention for monitoring ion concentrations, such as sodium (Na+) and potassium (K+), across various fields, including environmental monitoring, clinical diagnostics, food quality control and even sweat monitoring. However, multiplexed sensing of such ions with high sensitivity and selectivity is still challenging. Therefore, this work presents a multiplexed sensing of ions with high sensitivity and selectivity utilizing PEDOT: PSS OECTs integrated with ion-selective membranes (ISMs). First, a microscale fabrication method for manufacturing OECT arrays based on PEDOT: PSS is described, and then the integration of Na+ and K+ISMs on OECT microarrays using the spin coating technique is introduced. A microfluidic cell was integrated with the OECTs for real-time measurement of Na+ and K+ ion concentrations in a controlled flow-through manner. Following this, the influence of the membrane composition and thickness on the sensing performance of the OECTs was statistically investigated. The OECTs displayed a consistent linear response towards the detected ion type in a concentration range from 1 to 100 mM, while exhibiting notable selectivity against the undesired ions. Our results indicate that a reduction in membrane composition and thickness leads to an increase in sensitivity, with the drawback of a decrease in selectivity for ion concentration detection. We optimized the ISMs for both ion types and utilized them on one and the same array for multiplexed monitoring of Na+ and K+ ion concentrations.