PURPOSE To clarify the long-term effect of topical antibiotics on the ocular bacterial flora after cataract surgery. SETTING Miyata Eye Hospital, Miyazaki, Japan. DESIGN Prospective case series. METHODS Patients who had cataract surgery between November 2014 and January 2015 were included. Levofloxacin 1.5% was administered 4 times a day by topical instillation from 3 days before surgery to 1 month postoperatively. The conjunctival sacs of patients were scraped before the procedure and 0, 3, 6, 9, and 12 months after the last instillation. The samples were cultured, and minimum inhibitory concentrations (MICs) of levofloxacin for Staphylococcus epidermidis and Propionibacterium acnes were evaluated using mixed-effects models. RESULTS The study evaluated 50 patients. Diverse bacterial species, predominantly S epidermidis and P acnes, were isolated before the application of topical levofloxacin. Bacterial diversity was substantially reduced after the final topical levofloxacin application and subsequently increased after 3 months. However, the geometric mean levofloxacin MICs for S epidermidis isolates were still significantly higher at 0 months and 3 months than before treatment (P < .01 and P = .03, respectively) and reached pretreatment levels 6 months and 12 months after the last application. Propionibacterium acnes did not show significant changes in the geometric mean levofloxacin MIC over time. CONCLUSION The restoration of the bacterial flora required more than 6 months after cataract surgery and topical levofloxacin.