Malnutrition alters metabolism and immunity, affecting one's ability to fight infections and influencing clinical outcomes. To quantify differences in infection dynamics among groups of different nutrition statuses and challenged with different viruses, we developed within-host mathematical models of acute infections and fitted them to data from mice fed either a high-fat overnutrition diet, a low-protein undernutrition diet, or a lean control diet and infected with either Mayaro, Ross River or chikungunya. In addition to finding virus-specific host-virus dynamics, model analyses showed decreased infected cell removal rates in undernourished infected mice compared to overnourished infected mice, regardless of the pathogen. Additionally, we found lower viral production rates in undernourished infected mice compared to overnourished infected mice, in two out of the three virus infections. These results suggest that diet is an important factor in understanding viral-host interactions, and should be considered when designing interventions.