The architecture of genetic variation underlying phenotypic traits is a complex interplay between the environment (e.g., diet) and host genome. However, the specific impact of the environment and its interaction with the host genome on phenotypic traits is poorly understood. To address this knowledge gap, we fed 1,154 mice from an autoimmunity-prone advanced intercross line different diets across multiple generations. We found that diet substantially contributed to phenotypic variation and unmasked novel genetic susceptibility loci. Notably, diet contributed not only to the variation in metabolic phenotypes but also to various immunological phenotypes. By performing whole-genome sequencing of the founder mouse strains, we resolved several QTL, which still encompassed multiple genes, to single candidate genes. In addition to novel associations, several of the identified genes have been reported in human genome-wide association studies (GWAS). To determine the functional relevance of the diet-induced shift in genetic association, we set lupus-prone NZM2410/J mice on different diets. We show that diet overrides genetic disease susceptibility by modulating intestinal bacterial and, interestingly, fungal communities, which in turn, alter the transcriptome. Herein, using a multi-omics approach, we identified a single diet-regulated gene for the production of antinuclear antibodies, namely, Tnxb. Collectively, our study urges the inclusion of environmental factors in GWAS to unveil hidden genetic susceptibility.