Brazil is currently one of the largest soybean and maize producers in the world. A dramatic increase in total production of these grains was possible due to the implementation of double cropping systems (two crops on the same land in the same agricultural calendar) in places where the wet season is sufficiently long. Although several recent studies have assessed soybean productivity change in South America after climate change, they have not considered important factors such as the decision whether or not to adopt double cropping systems and the incidence of diseases—both of which can influence planting dates. Here, we test five cultivars (expressed by total growing degree days) and 10 planting dates using two crop models and four climate models to assess soybean productivity in Brazil after climate change. Our results indicate that soybean productivity will increase in farms that choose to grow only one crop in the agricultural calendar (planting dates occur usually in November–December). However, the productivity of short-cycle cultivars planted in late September, typically sowed by farmers who chose to grow two crops in the same agricultural calendar, may dramatically decrease. While delaying planting dates of early planted cultivars can offset productivity loss, it may also compromise the possibility to plant a second crop. Furthermore, additional deforestation can lead to increased productivity loss due to further reductions in September and October rainfall. Urgent adaptation strategies are needed to maintain highly productive double cropping systems in Brazil in the advent of climate change.