Bats serve as important reservoir hosts for many important zoonotic viruses and a better understanding of their ecology would be beneficial in preventing disease spillover to other species, including humans. This dissertation explores the factors that influence viral shedding in bats, which is a critical step in the spillover of zoonotic viruses. Using hierarchical Bayesian modeling, we show that individual wild black flying foxes (Pteropus alecto) that are consuming a more diverse diet and have markers of urinary tract inflammation are more likely to shed Hendra virus. This supports hypotheses that food stress and toxin exposure increase viral shedding risk. We next showed experimentally that changing the diet then infecting captive Jamaican fruit bats (Artibeus jamaicensis) with H18N11 influenza A virus can influence viral shedding patterns. In the future, we will further explore how diet led to different shedding patterns. Overall, this dissertation provides evidence that dietary changes and other physiological stressors can modulate bat immune function and viral shedding dynamics, increasing spillover risk.