The study purpose was to assess the efficacy of a preservative-free 0.6% povidone iodine eye drops as perioperative prophylactic treatment for reducing conjunctival bacterial load and the rate of needle contamination in patients undergoing intravitreal anti-vascular endothelial growth factor injection. Enrolled patients were randomized to either the study group (0.6% povidone iodine, three day-prophylactic treatment before the injection) or to the control group (placebo, three day-prophylactic treatment). Conjunctival swabs were obtained before and after the prophylactic treatment in both groups. Intravitreal injections were performed in a sterile fashion. The injection needle and a control needle were collected for microbiological culture. Data from 254 and 253 eyes in the study group and control group, respectively, were analyzed. Bacterial growth from conjunctival swab cultures was significantly lower after 0.6% povidone iodine prophylaxis compared to baseline and to placebo prophylaxis (p < 0.001), showing an 82% eradication rate in the study group. No injection needle showed bacterial contamination in the study group, whereas six needles were culture-positive in the control group (p = 0.015). No serious ocular and non-ocular adverse events were recorded. The 0.6% povidone iodine solution proved an effective treatment in reducing conjunctival bacterial load and risk of needle contamination.