Pistachio nuts are an important economic tree nut crop which is used directly or processed for many food-related activities. They can become colonized by mycotoxigenic spoilage fungi, especially , mainly resulting in contamination with aflatoxins (AFs), especially aflatoxin B (AFB). The prevailing climate in which these crops are grown changes as temperature and atmospheric CO levels increase, and episodes of extreme wet/dry cycles occur due to human industrial activity. The objectives of this study were to evaluate the effect of interacting Climate Change (CC)-related abiotic factors of temperature (35 vs. 37 °C), CO (400 vs. 1000 ppm), and water stress (0.98-0.93 water activity, a) on (a) growth (b) and biosynthetic gene expression and (c) AFB production by two strains (AB3, AB10) in vitro on milled pistachio-based media and when colonizing layers of shelled raw pistachio nuts. The strains were resilient in terms of growth on pistachio-based media and the colonisation of pistachio nuts with no significant difference when exposed to the interacting three-way climate-related abiotic factors. However, in vitro studies showed that AFB production was significantly stimulated ( < 0.05), especially when exposed to 1000 ppm CO at 0.98-0.95 a and 35 °C, and sometimes in the 37 °C treatment group at 0.98 a. The relative expression of the structural gene involved in AFB biosynthesis was decreased or only slightly increased, relative to the control conditions at elevated CO, regardless of the a level examined. For the regulatory gene expression, there was a significant ( < 0.05) increase in 1000 ppm CO and 37 °C for both strains, especially at 0.95 a. The in situ colonization of pistachio nuts resulted in a significant ( < 0.05) stimulation of AFB production at 35 °C and 1000 ppm CO for both strains, especially at 0.98 a. At 37 °C, AFB production was either decreased, in strain AB3, or remained similar, as in strain AB10, when exposed to 1000 ppm CO. This suggests that CC factors may have a differential effect, depending on the interacting conditions of temperature, exposure to CO and the level of water stress on AFB production.