Food systems are increasingly challenged to meet growing demand for specialty crops due to the effects of climate change and increased competition for resources. Here, we apply an integrated methodology that includes climate, crop, economic and life cycle assessment models to US potato and tomato supply chains. We find that supply chains for two popular processed products in the United States, French fries and pasta sauce, will be remarkably resilient, through planting adaptation strategies that avoid higher temperatures. Land and water footprints will decline over time due to higher yields, and greenhouse gas emissions can be mitigated by waste reduction and process modification. Our integrated methodology can be applied to other crops, health-based consumer scenarios (fresh versus processed) and geographies, thereby informing decision-making throughout supply chains. Employing such methods will be essential as food systems are forced to adapt and transform to become carbon neutral due to the imperatives of climate change.