In this work, we report polyimide-based biocompatible and flexible pH micro-probes. The sensing electrodes were based on iridium oxide (IrOx) thin film, electrodeposited by a cyclic voltammetry process onto a base sputtered gold (Au) layer. Square electrode configurations with sizes of 1 mm², 500 μm², 300 μm², and 200 μm² were designed, fabricated and tested; these yielded sensitivities of ~71 mV/pH, ~62 mV/pH, ~52 mV/pH and ~51 mV/pH, as well as limit of detection (LOD) values of 0.04 pH, 0.047 pH, 0.065 pH and 0.075 pH, respectively. Reference electrodes (REs) were developed by applying AgCl paste onto Au electrodes, followed by a curing process; demonstrating a comparable performance to commercial REs. Our pH micro-sensors hold promise for various applications, from analyses of chemical processes, to in-vitro and in-vivo experiments, to environmental or food safety monitoring.