This study reports on the effect of atmospheric pressure plasma jet treatment on the flax fiber and flax-reinforced epoxy. The atmospheric pressure plasma jet was carried out by using four different gasses and various application distance in the range of 30–40 mm. The treatments were investigated by means of contact angle, attenuated total reflectance–Fourier transform infrared spectroscopy, atomic force microscopy, scanning electron microscopy and mechanical tests. Depending on the application parameters, the rate of increase in water contact angle varied from 49% to 92%. While atomic force microscopy and scanning electron microscopy investigations exhibited changed surface morphology, FTIR presented interactions at the molecular level. Improvement in mechanical properties was obtained for all atmospheric pressure plasma jet applications, while the increase in tensile strength in the composite material reached 180%, and the increase in flexural strength was 140%. The atmospheric pressure plasma jet method, according to similar plasma applications, came to the forefront with the short processing time and the intensity of the effect it created.