We evaluated the persistence and efficacy of two different, in granulometry and content of diatoms, diatomaceous earth (DE) formulations (i.e., DE5 and DE6), against two major beetle species of stored products, i.e., Sitophilus oryzae (L.) (Coleoptera: Curculionidae) and Rhyzopertha dominica (F.) (Coleoptera: Bostrychidae). The formulations were applied as powders in soft wheat and maize in two doses of 500 and 1000 mg kg−1 (ppm). Samples of the treated grains were taken on the day of application and every 30 days until completion of the six-month period of storage. Adults of S. oryzae and R. dominica were exposed to the treated grains at 25 °C and 55% relative humidity, and the mortality was measured after 7, 14, and 21 days of exposure. Rhyzopertha dominica survival was not affected by any combination of DE formulation, dose, and commodity. Contrariwise, the DEs caused significant adult mortality of S. oryzae, in most of the cases tested. We observed that DE6 was equally effective in both wheat and maize, and no considerable variations were observed in S. oryzae mortality during the 6-month experimental period. Furthermore, DE6 was more effective against S. oryzae than DE5, a difference that could have potentially contributed to the variations in the diatom granulometry between these two DEs. Thus, a DE treatment of 1000 ppm was shown to provide long-term protection of wheat and maize against S. oryzae, but this is strongly dependent on the DE formulation, commodity, and insect species. Overall, such natural resource-based inert silicaceous deposits could be used with success in stored-product protection with only some minor modifications, such as sieving and drying of the raw deposit.