Introduction Inflammatory bowel diseases (IBD) are characterized by chronic intestinal inflammation that potentiates the risk for developing colorectal cancer. Indeed, single nucleotide polymorphisms in NOD-like receptor (NLR) family pyrin domain containing-3 (NLRP3) gene has been linked to increased susceptibility to IBD in humans. However, the regulatory mechanisms of NLRP3 signaling pathways leading to the intestinal inflammation in IBD are not well defined. Previous studies have shown that Protein Kinase R (PKR), a kinase mediating stress response via phosphorylation of the eukaryotic initiation factor 2α (eIF2α), enhances Toll-like receptor signaling which is required to prime NLR inflammasomes. Here we tested the role of PKR in the NLR signaling pathway and its consequence to intestinal inflammation. Methods Wild-type (WT) or PKR-ablated mice were treated with dextran sodium sulphate in their drinking water and their condition monitored daily. After 9 days intestinal tissue sections were taken from both mouse strains and compared. Additionally, immortalized spleen and primary peritoneal macrophages from WT and PKR-ablated mice were primed with the Toll-like receptor 4 (TLR4) ligand lipopolysaccharide (LPS) for 4 h, and treated with NLR3 ligands for 1–2 h. Then, cell culture supernatants were analyzed for production of inflammatory cytokines. Results While WT mice demonstrated no conspicuous symptoms, PKR-ablated mice exhibited clinical symptoms of pathology and lost 20% of their weight by day 9. Correspondingly, the PKR-ablated mice had enhanced intestinal tissue damage when compared to WT mice. We showed that although similar levels of IL1β are induced in WT and PKR-ablated macrophages, higher levels of total IL-1β was released from PKR-ablated macrophages upon stimulations with nigercin or calcium pyrophosphate dehydrate crystals. In keeping with this, we show increased cleavage of pro-IL-1β to the active form in the absence of PKR. Moreover, activation of caspase-1 (CASP1), the protease that processes IL-1β, was increased in PKR-ablated compared to WT cells. Using kinase-dead PKR, we show that this repression of the inflammasome in part requires substrate phosphorylation. Conclusion We revealed that PKR is protective in a murine model of colitis and show this is due to repression of the activity of the NLRP3 inflammasome. These findings may provide insight into the development of therapeutic strategies against IBD.