ABSTRACT Purpose To review the presentation and visual prognostic factors of patients with endogenous endophthalmitis before and after the introduction of microincision vitrectomy surgery (MIVS), at a tertiary referral hospital in Taiwan, over a 21-year period. Methods We retrospectively analyzed medical records of patients diagnosed with endogenous endophthalmitis before and after the introduction of MIVS between January 2002 and December 2022. Results Data were collected from 147 patients. Diabetes mellitus was the most common comorbidity (59.9%). Liver abscess (32.7%) was the leading source of infection, followed by urinary tract infection (15.0%), and infective endocarditis (5.4%). Klebsiella pneumoniae (50.4%) was the most common pathogen, followed by Staphylococcus aureus (13.5%), and Candida albicans (8.3%). Poor initial visual acuity worse than counting fingers (CF) (p < 0.001) and diabetes mellitus (p = 0.008) were significantly associated with poor visual outcomes. In the treatment of 98 patients with poor initial visual acuity worse than CF, the proportion of vitrectomy surgeries performed increased from 13/56 (23.2%) to 24/42 (57.1%) (p = 0.001) after the introduction of MIVS. Final visual acuity of CF or better increased from 7/56 (12.5%) to 12/42 (28.6%) after the introduction of MIVS (p = 0.046). Vitrectomy was a better prognostic factor for final visual outcome in patients with poor initial visual acuity of worse than CF (p = 0.011) than other factors. Conclusion In endogenous endophthalmitis patients presenting with poor initial visual acuity, vitrectomy was a better visual prognostic factor. MIVS has allowed more patients to undergo vitrectomy and improved visual outcomes.