Omega-3 polyunsaturated fatty acids (n-3 PUFAs), which are key components of fish oil, are increasingly consumed for their health benefits and have been shown to dramatically influence chronic disease. Although omega-3s can lead to the production of less inflammatory metabolites, we focused on the direct effects of a high omega-3 diet on T cell activation during viral infection. Specifically, we analyzed T cell recognition of antigen and the resulting functional responses during lymphocytic choriomeningitis (LCMV) infection. The omega-3 based diet manipulated structural lipid content in plasma membranes leading to reduced T cell frequency and changes in the prevalence of immunodominant epitopes. We further found that a high omega-3 diet decreased 2D affinity and number of tetramer positive polyclonal as well as CD8 T cell receptor transgenic cells at peak anti-viral immunity. In addition to affinity, the bond lifetime of antigen recognition was also decreased. This resulted in decreased numbers of SLEC and effector cytokines without impeding viral clearance. Our work indicate that a major effect of dietary omega-3 fatty acids on T cells is the modification of the cell membrane to dampen the initial recognition of antigen leading to decreased but effective immunity.