Mucosal sites, such as the intestine, constantly interact with non-self entities and distinguish between microorganisms that are beneficial, like the microbiota, or pathogenic, like viruses. There are many unexplored mechanisms of how the intestine recognizes the microbiota and the influence this has on the intestinal response to pathogen challenge. If a pathogen overcomes the multitude of cell autonomous immune mechanisms of the intestinal epithelium, then it gains access to the host body cavity and organs which launch their own immune responses to protect the host organism. However, how the microbiota influences systemic virus challenge and how the immune response varies between tissues has been underexplored. The Cherry lab previously developed Drosophila melanogaster as a model to study enteric virus infection and the microbiota. In this dissertation, we further explore antiviral signaling in the intestine and whole animal and the microbiota’s influence on oral and systemic immunity. We first found autophagy genes, like Atg16, and the ancient antimicrobial protein Drosophila STING (dSTING) are antiviral in the intestine against the alphavirus Sindbis virus (SINV) and a picorna-like virus Drosophila C virus (DCV). Similarly, cyclic dinucleotides (CDNs), the molecules that bind and activate STING, are antiviral during enteric oral infection and induce gene expression changes that are dependent on dSTING and inflammatory NF-kB signaling. CDNs are molecules that must be actively transported into cells, and we identified a putative CDN transporter that is antiviral in enterocytes and is required for CDN-mediated protection from infection and induction of gene expression changes. In contrast to oral infection, we find that autophagy genes, dSTING, the microbiota, and cyclic dinucleotides do not protect flies from systemic SINV infection. Despite this, during systemic DCV infection dSTING and CDNs protect flies while loss of the microbiota exacerbates infection. This uncovers both tissue and virus specific immune responses. Overall, this work defines previously unknown antiviral mechanisms in the fly intestine, explores how the microbiota and bacterial derived products influence enteric and systemic virus infection, and differentiates tissue responses to virus infection.