In this study, we investigate the keys to obtain a sensitive ammonia sensor with high air stability by using a low-cost polythiophene diode with a vertical channel and a porous top electrode. Poly(3-hexylthiophene) (P3HT) and air-stable poly(5,5'-bis(3-dodecyl-2-thienyl)-2,2'-bithiophene) (PQT-12) are both evaluated as the active sensing layer. Two-dimensional current simulation reveals that the proposed device exhibits numerous connected vertical nanometer junctions (VNJ). Due to the de-doping reaction between ammonia molecules and the bulk current flowing through the vertical channel, both PQT-12 and P3HT VNJ-diodes exhibit detection limits of 50-ppb ammonia. The P3HT VNJ-diode, however, becomes unstable after being stored in air for two days. On the contrary, the PQT-12 VNJ-diode keeps an almost unchanged response to 50-ppb ammonia after being stored in air for 25 days. The improved storage lifetime of an organic-semiconductor-based gas sensor in air is successfully demonstrated.