The resilience of the microbiome determines whether the community returns to the original steady state or to an altered state after perturbation. Microbiome resilience can have positive or negative outcomes for the host, including maintaining resistance to Clostridioides difficile infection after exposure to antibiotics or contributing to the development of chronic disorders including inflammatory bowel disease. In this study, we used longitudinal sampling of antibiotic-treated mice to characterize the resilience of both the viral and bacterial populations of the intestinal microbiome. Our results revealed that viral populations were significantly more dynamic than bacterial populations during recovery, suggesting the viral community is less resilient than the bacterial community. These studies lead to a greater understanding of intestinal microbiome resilience and have the potential to impact current treatment practices and improve patient health outcomes.