Degrading purine nucleosides in wort into free purines to facilitate yeast absorption has been proven effective for reducing purine in beer. In this study, a probiotic strain of Pediococcus acidilactici GR-5, isolated from traditional fermented foods in northwest China, was found to completely degrade adenosine, guanosine, and inosine within 12 h. Using GR-5 post-fermentation to produce beer, the contents of purine nucleoside and purine in beer were reduced by approximately 80.15% and 41.91%, respectively. The purine metabolic pathway of GR-5 was upregulated during the fermentation process, enhancing the beer’s fruity flavor with minimal impact on overall volatile flavor. GR-5 in low-purine live bacteria beer mitigates beer-induced serum UA elevation, liver and kidney damage, and inflammatory factor levels by regulating renal UA synthase, antioxidant indicators, and the NLRP3 inflammatory pathways. GR-5 also colonizes the mouse intestine, enhancing the purine metabolism of gut microbiota and increasing the abundance of probiotics. This technology offers a novel approach for the production and technical optimization of low-purine beer.