Purpose: Blood culture contamination (BCC) is mainly caused by commensal bacteria, during sample collection. It results in unnecessary antibiotic exposure, prolonged hospitalisation, additional microbiology workup and significant adverse health-economic burden. We aimed to investigate the short- and long-term impact of the COVID-19 pandemic on the incidence of BCC. Methods: We conducted a retrospective, observational cohort study at Geneva University Hospitals (HUG). We included all BCCs from January 2018 to December 2023, collected as part of a prospective hospital-wide surveillance by the infection control team. Data were analyzed using segmented Poisson regression models to evaluate BCC incidence rate ratios (IRRs) across three periods: pre-COVID-19 (2018–2019), during COVID-19 (2020–2021), and post-COVID-19 peak (2022–2023). Results: Out of 456,873 collected blood cultures, 1,247 BCCs were identified (0.27%). The contamination rate per 1000 samples increased from 1.53 pre-COVID-19 to 2.94 during COVID-19 and 3.52 post-COVID-19. Compared to the pre-COVID-period, incidence rate ratios (IRRs) for BCC increased during COVID-19 (IRR 1.84, 95% CI 1.58–2.15) and post-COVID-19 peak (IRR 2.29, 95% CI 1.97–2.66). During COVID-19, proportions of BCC were increased in intensive care units (27.4%, n = 127) and returned to baseline level post-COVID-19 (17.3%, n = 93, p < 0.001); whereas, in other wards, BCC remained elevated (42.2%, n = 227) in the post-COVID-19 period. Conclusions: We observed a significant rise in BCC incidence during and after the COVID-19 peak. The persistently elevated post-peak rates highlight ongoing challenges in regaining optimal aseptic blood culture collection practices and the need for further exploration of persisting factors increasing BCC rates.