Atmospheric plasma jets generated from air or nitrogen using commercial sources with relatively high energy densities are commonly used for industrial applications related to surface treatments, especially to increase the wettability of polymers or to deposit thin films. The heat fluxes to which the substrates are subjected are typically in the order of 100–300 W/cm$^2$, depending on the treatment conditions. The temperature rise in the treated polymer substrates can have critical consequences, such as a change in the surface crystallinity or even the surface degradation of the materials. In this work, we report the phase transitions of two semicrystalline industrial-grade polymer resins reinforced with glass fibers, namely polyphenylene sulfide (PPS) and polyphthalamide (PPA), subjected to plasma treatments, as well as the modeling of the associated heat transfer phenomena using COMSOL Multiphysics. Depending on the treatment time, the surface of PPS becomes more amorphous, while PPA becomes more crystalline. These results show that the thermal history of the materials must be considered when implementing surface engineering by this type of plasma discharge.