Probiotic bacteria is able to metabolize polyphenols and produce functional compounds. In this study, we investigated the ability of probiotic bacteria including Lactobacillus, bifidobacteria and Enterococcus strains to increase the antioxidant capacity of polyphenols from lotus seed epicarp (PLSE) at full ripening stage. The results showed that the six selected strains of probiotic bacteria grew well in De Man, Rogosa and Sharpe (MRS) broth with PLSE, and their resistant extent to PLSE varied from strain to strain. The metabolized PLSE was found to have good antioxidant properties on 3-ethylbenzothiazoline-6-sulfonic acid (ABTS+) and 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals in vitro. Five polyphenol compounds—chlorogenic acid, caffeic acid, catechin, epicatechin and hyperoside—were suggested as the major bioactive metabolism for the antiradical activity of PLSE metabolized by Lactobacillus reuteri DSM20016, Enterococcus faecalis M74 and Bifidobacterium breve ATCC 15701. Moreover, L. reuteri DSM20016 and E. faecalis M74 were found to have a high PLSE bioconversion rate. Our results suggested that both L. reuteri DSM20016 and E. faecalis M74 might have excellent potential for the bioconversion of PLSE to increase its antiradical activity.