The introduction of transgenic cotton (Bt-cotton) for controlling bollworms has resulted in increased production; however, the residual effects of mulches from Bt-cotton are poorly understood. Therefore, the current study evaluated the impact of Bt and non-Bt cotton mulches on soil properties, weed dynamics and yield of winter crops sown after cotton. Three different winter crops, i.e., wheat (Triticum aestivum L.), canola (Brassica napus L.) and Egyptian clover (Trifolium alexandrinum L.) and two mulch types, i.e., Bt mulch (obtained from Bt-cotton cultivars, i.e., 'CIM-616' and 'GH-Mubarik') and non-Bt mulch (obtained from non-Bt cultivars, i.e., 'CIM-620' and 'N-414') were included in the study. The mulches were applied at a rate of 2 t ha-1 before planting the winter crops. The Bt and non-Bt mulches differentially affected soil properties, weed dynamics and productivity of winter crops. The non-Bt mulches decreased the soil bulk density and penetration resistance, while increased the soil porosity. Wheat crop increased the soil porosity, pH, available N and soil organic matter content. Overall, non-Bt mulches improved the productivity of winter crops compared with Bt mulches. The toxins released by Bt mulches lowered the weed density; however, it negatively influenced soil properties (bulk density and available nitrogen) and productivity of winter crops. Therefore, appropriate crop rotation measures may be opted for the soils cultivated with Bt-cotton to conserve soil and achieve yield sustainability for the crops sown after cotton. Nonetheless, non-Bt mulches can be used for improving soil properties and productivity of winter crops.