Maize (Zea mays L.), a food crop cultivated worldwide, is renowned for its nutritional and economic value. However, its quality can be significantly affected by various storage conditions, leading to changes in its nutritional composition and potential contamination with harmful substances, such as aflatoxins. This article presents a comprehensive evaluation of the impact of storage on maize quality, focusing on several key parameters analyzed using liquid chromatographic methods and FT-NIR spectrometry. The research reveals a decline in the concentrations of key nutrients over the storage period. Specifically, there was a 19.7% loss in vitamin B1, a 12.43% loss in vitamin B3, a 16.96% loss in α-tocopherol, a 13.61% loss in total tocopherols, and an 8.02% loss in β-carotene. Aflatoxins were mostly undetectable, with one exception in January that remained below the maximum permitted level of 0.3 µg/kg. The parameters include the concentration of vitamins B1, B3, α-tocopherol, total tocopherols, β-carotene, aflatoxin B1, total aflatoxins, carbohydrate content, and protein content. Aflatoxins were mostly undetectable, with one exception in January—0.3 µg/kg—that remained below the maximum permitted level. The study underscores the importance of cooling maize immediately after drying to minimize nutrient loss, providing valuable insights for optimizing storage processes to maintain the nutritional quality of maize.