Smallholder farmers in Northern Ghana face challenges due to weather variability and market volatility, hindering their ability to invest in sustainable intensification options. Modeling can help understand the relationships between productivity, environmental, and economical aspects, but few models have explored the effects of weather variability on crop management and resource allocation. This study introduces an integrated modeling approach to optimize resource allocation for smallholder mixed crop and livestock farming systems in Northern Ghana. The model combines a process-based crop model, farm simulation model, and annual optimization model. Crop model simulations are driven by a large ensemble of weather time series for two scenarios: good and bad weather. The model accounts for the effects of climate risks on farm management decisions, which can help in supporting investments in sustainable intensification practices, thereby bringing smallholder farmers out of poverty traps. The model was simulated for three different farm types represented in the region. The results suggest that farmers could increase their income by allocating more than 80% of their land to cash crops such as rice, groundnut, and soybeans. The optimized cropping patterns have an over 50% probability of increasing farm income, particularly under bad weather scenarios, compared with current cropping systems.