Background The availability of good quality seeds is synonymous with improved farming, especially cash crops such as cotton. However, serious problems with seed germination have been reported recently by cotton farmers in Benin Republic. The assumptions formulated at the base with regard to this situation remain to be verified technically. Thus, this study aims to evaluate the influence of storage conditions on the quality of cotton seeds in Northern Benin. Temperature and relative humidity were assessed followed by a seed sampling sequence in seven (07) cotton seeds stores according to three main periods, ranging from the establishment in conservation to the following seasonal production. Germination tests were then carried out on each sample followed by data analysis using R and Minitab17 software.Results There is a large variation in the germination rate of cotton seed during their storage period. The probabilities values ​​(Pvalue1 = 0.023, Pvalue2 = 0.001 and Pvalue3 = 0.038) respectively associated with the three samples and the various coefficient of variation (CV) between stores (CV1 = 2.42%, CV2 = 7.1% and CV3 = 8.88%) explain a significant difference not only between the stores but also from one sample to another with regard to sampling periods. There is a strong progressive decrease in seed germination (Germination rate 1 > Germination rate2 > Germination rate3), which is responsible for the failure observed by the growers during sowing. Thus, seeds lose an average of 15% of their initial germination capacity already at one month of storage. This is generally negative due to all the storage conditions and system in the stores.Conclusions The excessive increase in temperature and the considerable decrease in relative humidity in stores are the main factors of significant loss of germination capacity of cotton seeds. In view of this situation, it is desirable that technical measures be taken in this direction in order to better preserve the quality of the seeds made available to producers for an optimization of the cotton sector in Benin.