The purpose of this study was to analyze the effect of warehouse management on the organizational performance in a manufacturing company. Despite the many efforts used by Rwandan manufacturing industries in warehouse management to store their goods, equipment, inventory, and other items, the achievement remains uncertain, and this affects poorly the performance of Cimerwa Limited. In conducting this research, three objectives were focused on: to assess the effect of inventory on performance of Cimerwa Limited in Rusizi District, to find out the effect of material handling, packing and dispatching on performance of Cimerwa Limited in Rusizi District and finally to assess the effect of automation and optimization on performance of Cimerwa Limited in Rusizi District. To achieve these objectives, literature was reviewed on the subject matter, and then data was collected from 285 employees of Cimerwa Cement and out of them a sample size of 166 respondents were selected by using purposive sampling technique. Questionnaire, observation, interview guide and documentation were used as tools of data collection. Data was analyzed by using both quantitative data and qualitative data by presenting the findings of respondents through the mean and standard deviation. The R Square value, at 0.792, signifies that 79.2% of the variation in organizational performance can be explained by the combined influence of automation and optimization, inventory, and material handling. Regarding inventory, it displays an unstandardized coefficient β of 0.676, with a highly significant p-value of 0.000<0.05. Similarly, for material handling, the unstandardized coefficient β is 0.731, and the effect is statistically significant with a p-value of 0.000<0.05. Likewise, for automation and optimization, the unstandardized coefficient β is 0.666, and the effect is statistically significant with a p-value of 0.000<0.05. Cimerwa should improve inventory management, implement efficient production planning, and enhance warehouse management for better organizational performance, incorporating techniques like EOQ and JIT for cost savings. The study concluded that there is a positive link between warehouse management and the organizational performance of Cimerwa; thus, the warehouse at Cimerwa moves, stores, tracks, and ships items. Therefore, inline of findings researcher recommended that Cimerwa must also ensure that a good production plan is used.