Povidone‑iodine (PVP-I) is a disinfectant widely used to prevent and treat bacterial diseases in fish. The use of PVP-I may disturb the microbial community on the fish body surface and thereby facilitate pathogen invasion. We aimed to assess the effects of PVP-I on the immune system and bacterial communities of skin and gill in Cyprinus carpio. Fish were disinfected with 7.5 mL/m3 of PVP-I (1%) for 30 min, and then skin and gill tissues were sampled on days 0, 1, 3, 7, and 14 for the determination of immunity parameters and characterization of surface bacterial communities. Control fish were not disinfected. The results indicated that exposure to PVP-I decreased the activities of gill lysozyme on day 1, and significantly increased the activities of gill SOD and Na-ATPase on day 7. The activity of skin SOD was enhanced on day 3. The PVP-I bath enhanced the mRNA expression of lysozyme, sod, and cat in the gill but decreased lysozyme on days 1–7 and sod on days 7–14 in the skin. The mRNA expression of tight junction proteins was enhanced in both gill and skin tissue. PVP-I decreased gill bacterial richness on days 3 and 7, and reduced bacterial diversity on day 7. The gill microbiota on day 7 was remarkably separate from the control. The skin microbiota on days 1 and 3 was significantly separated from that of the control. In summary, PVP-I elicited shifts in the immune response and changes in the surface microbiota of fish, and the sensitive time windows of microbial fluctuation after PVP-I treatment were three days in the skin and seven days in the gill.