Post-harvest losses due to insect infestation and spoilage by bacteria and molds pose significant challenges to global cereal production. This study investigates the prevalence of resistance to phosphine, a commonly used grain protection agent, in stored-grain insects. The research, conducted in various storage facilities across Greece, examined 53 populations of key stored-product insect species. Two assessment protocols, namely, dose–response (at 50–1000 ppm for 3 days exposure) and CORESTA (at 300 ppm for 6 days), were used herein to estimate phosphine resistance. The results showed that 13.3% of field populations were resistant, and mortality rates increased with higher phosphine concentrations. Specifically, according to the dose–response protocol, among the 53 field populations, 37.7% were found to be resistant to phosphine, namely, two populations of O. surinamensis, one of S. oryzae, seven of T. confusum, one of C. ferrugineus, one of T. castaneum, and all populations of R. dominica, whereas, according to the CORESTA protocol, all populations were found to be susceptible to phosphine. The observed resistance patterns differ from those reported in other regions of the world. The study highlights the importance of tailored fumigation strategies, considering insect species varying susceptibility to phosphine. It recommends the use of best management practices and rotational strategies, such as combining phosphine with other methods, to develop effective resistance management plans. The results provide valuable insights into the dynamic landscape of phosphine resistance in stored-product insects and suggest potential avenues for further research and control measures.