Adapting organic farming to climate change is a major issue. Cotton yields in Mali are declining due to deteriorating climatic conditions, soil fertility, and poor management. This study aimed to improve organic cotton yield in Mali in the future climate with the optimal choice of compost type, date, and dose of application. Experimental data collected in 2021 from the Sotuba research station in Mali was used for calibration and evaluation of the crop model DSSAT CSM-CROPGRO-Cotton model using phenology, leaf area index, and seed cotton yield. Climate data from the RCP4.5 and RCP8.5 scenarios of the GFDL-ESM2M model were used for future weather datasets for 2020-2039, 2040-2059, and 2060-2079. The model was able to simulate anthesis and maturity with excellent results, with nRMSE < 4%, and seed cotton yields moderately well, an nRMSE of 26% during calibration and 20.3% in evaluation. The scenario RCP8.5 from 2060 to 2079 gave the best seed cotton yields. Seed cotton yields with RCP4.5 and RCP8.5 were all better with the mid-May application period of small ruminant silo compost at 7.5 t/ha. In such conditions, more than 75% of the cases would produce more than 2000 kg/ha of seed cotton.