The combustion of agricultural storage represents a big hazard to the safety and quality preservation of crops during lengthy storage times. Cotton storage is considered more prone to combustion for many reasons, i.e., heat by microbial growth, exothermic and endothermic reactions in storage areas, and extreme weather conditions in storage areas. Combustion not only increases the chances of a big fire outbreak in the long run, but it may also affect cotton’s quality factors like its color, staple length, seed quality, etc. The cotton’s quality attributes may divert from their normal range in the presence of combustion. It is difficult to detect, monitor, and control combustion. The Internet of Things (IoT) offers efficient and reliable solutions for numerous research problems in agriculture, healthcare, business analytics, and industrial manufacturing. In the agricultural domain, the IoT provides various applications for crop monitoring, warehouse protection, the prevention of crop diseases, and crop yield maximization. We also used the IoT for the smart and real-time sensing of spontaneous combustion inside storage areas in order to maintain cotton quality during lengthy storage. In the current research, we investigate spontaneous combustion inside storage and identify the primary reasons for it. Then, we proposed an efficient IoT and machine learning (ML)-based solution for the early sensing of combustion in storage in order to maintain cotton quality during long storage times. The proposed system provides real-time sensing of combustion-causing factors with the help of the IoT-based circuit and prediction of combustion using an efficient artificial neural network (ANN) model. The proposed smart sensing of combustion is verified by a different set of experiments. The proposed ANN model showed a 99.8% accuracy rate with 95–98% correctness and 97–99% completeness. The proposed solution is very efficient in detecting combustion and enables storage owners to become aware of combustion hazards in a timely manner; hence, they can improve the storage conditions for the preservation of cotton quality in the long run. The whole article consists of five sections.