Uncertainty exists as to the role of fluoroquinolone (FQ) prophylaxis for patients undergoing allogeneic haematopoietic stem cell transplantation (HSCT) in the era of rising antibiotic resistance. We aimed to evaluate rates of bloodstream infections (BSI), resistance patterns and outcomes of patients after discontinuing routine FQ prophylaxis administration. All adult recipients of first HSCT from 2017 to 2020 were retrospectively included and classified according to time of HSCT as FQ group (HSCT January 2017-December 2018) or no FQ group (January 2019-December 2020). The primary outcome was Gram-negative (GN) BSI from day -7 to 30 days post-HSCT. The independent association between the study period and BSI was assessed using survival analysis, and adjusting for confounders. We included 254 patients, 130 (51%) and 124 (49%) in the FQ and no FQ groups, respectively. Compared to the FQ group, no FQ had significantly more GN BSI (21% versus 33%, P = 0.027) and the median time to first GN BSI was significantly shorter [4 (IQR 1-8) days versus 6 (1-10) days, P = 0.009]. Following adjustment, FQ prophylaxis remained associated with lower hazard for GN BSI (hazard ratio 0.57, 95% CI 0.34-0.93). Eighty-two GN BSI episodes had FQ susceptibility testing. More GN BSI episodes were FQ resistant in the FQ group (68.9% versus 41.6%, P = 0.021). No significant difference was found for 30-day mortality, time to first febrile neutropenia and time to first broad-spectrum antibiotics between the groups (P was not significant). FQ prophylaxis is associated with fewer GN BSI in the early post-HSCT period even in high FQ resistance settings, with FQ resistance rates reaching >60% following prophylaxis.