This study assessed potential impacts of climate on the dynamics of soybean-maize systems, a widespread cropping practice in Central Brazil, in regions of Mato Grosso state. Baseline (historical) and future climate scenarios in the mid and end of the twenty-first century were locally defined. Climate projections were input in a crop model, which was used to analyze their impact on first season's crop (soybean), and more emphasis was given on the second season's crop, maize development. In the climate projections, we observed a generalized increase in temperature for all scenarios, with variability of rainfall amount and pattern. Soybean growth showed a general enlargement of cycle length (average of up to 16%) and increase of yields (average of up to 34%) in future conditions. Soybean sowing dates and future climate contributed to the shortening of recommended maize sowing window and yield decreases. At most extreme scenarios of future climate, only soybean sown at the earliest dates would enable the latest maize sowing dates, bringing the greatest losses to the latter crop. Estimated maize yields showed relative average variations from baseline of − 22.5% and − 32.5% in RCP 4.5 in the mid and end of the century, while variations were of − 34% and − 55% in RCP 8.5 in the mid and end of the century, respectively. Timing of soybean sowing dates in a future climate will become more important in influencing the dynamics of subsequent maize's sowing dates and yields under a more extreme and unfavorable climate for its development.