Current ammonia sensors exhibit cross-sensitivity to water vapor, leading to false alarms. We developed a core–shell nanofiber (CSNF) structure to address these issues, using conductive poly(3,4-ethylenedioxythiophene) (PEDOT) as the core and hydrophobic polyvinylidene fluoride-tetrafluoroethylene (PVDF-TrFE) as the shell. The PEDOT-PVDF CSNF, with a diameter of ~500 nm and a 300 nm thick PVDF layer, showed a superior sensitivity and humidity resistance compared to conventional PEDOT membranes for ammonia concentrations of 10–100 ppm. In humid environments, CSNF sensors outperformed membrane sensors, exhibiting a tenfold increase in performance at 51% relative humidity (RH). This study highlights the potential of CSNF sensors for practical ammonia detection, maintaining a high performance under varying humidity levels.