The cytotoxic proteases Granzymes A (GzmA) and B (GzmB) are important components of the arsenal used by cytotoxic immune cells to kill virally infected/damaged cells. Until now, there has been limited evidence that GzmA/B proteins contribute to combating intracellular bacterial pathogens in mammals. Here, we find that the route of infection of the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium reveals the distinct roles that Granzymes play in defending against bacterial infection. We used Gzma-/-Gzmb-/- mice to discover that Granzymes are required to protect mice against oral infection with Salmonella. However, Granzymes do not play a role in systemic infection. We investigated the tissue-specific expression of Granzymes and determined that intestinal intraepithelial lymphocytes (IEL) are the only cell types that express Granzymes in healthy non-infected mice. In fact, IEL are sufficient to mediate the protective effects of Granzymes against Salmonella infection. Intriguingly, we found that GzmA and GzmB play opposing roles in Salmonella control, with GzmA being protective against infection whilst GzmB promoted infection. Both GzmA and GzmB proteins functioned independently of the pore-forming molecule Perforin, suggesting extracellular action. Our study reveals that IEL-expressed Granzymes play significant and distinct functions in host defense from oral bacterial infection.