Flexible microneedles are important tools that allow access to the inside of biological tissue from the outside without surgery. However, it had been hard to realize microneedle sensor arrays on flexible substrates because of the difficulty of attaining a needle with a high Young’s modulus for a selected area on a thin or soft substrate. In this work, we developed a microneedle sensor on a hybrid substrate based on high Young’s modulus epoxy siloxane for the microneedles and low Young’s modulus polydimethylsiloxane for the conformable substrate. Polyaniline was deposited on the microneedle for pH sensing. The mechanical durability of the device was assessed by insertion into pig skin 1000 times. Last, the flexible microneedle pH sensors showed their utility for monitoring pH distribution in rats in a peripheral artery diseases model.