Peanut production contributes to food security in northern Ghana due to its ability to tolerate drought and survive on marginal lands. This notwithstanding, poor handling along the value chain favors aflatoxin contamination, a threat to human and animal life. Farmer-led improved storage practice, a potential solution to aflatoxin contamination, have been promoted in northern Ghana. However, there is limited evidence on the factors influencing the use of the improved storage system that may guide dissemination efforts. Using the Cragg’s two stage model, our results show that the probability and intensity of adopting the improved storage structure is principally and significantly influenced by economic active household members, storing of peanut in other places relative to the field, and location of farmer residence. In disseminating the improved peanut storage structure, the identified factors must be incorporated in the selection criteria to ensure maximum uptake and usage. Farmer training programs that incorporate both good agronomic practices and good storage practices must be intensified to reduce postharvest losses due to aflatoxin contamination. These strategies will help mitigate the harmful effect of aflatoxin, ensure economic sustainability, and enhance food security.