Abstract Background Fluroquinolone prophylaxis during haematopoietic cell transplantation (HCT) remains contentious. Objectives To determine the effectiveness of ciprofloxacin prophylaxis across different HCT indications and its association with exposure to treatment antimicrobials and antimicrobial resistance. Methods All admission episodes for HCT (N=400) in a tertiary centre between January 2020 and December 2022 were studied. Allogeneic haematopoietic cell transplantation (allo-HCT) recipients received prophylaxis with ciprofloxacin during chemotherapy-induced neutropenia, while autologous haematopoietic cell transplantation (auto-HCT) recipients did not. Results Allo-HCT was performed for 43.3% (173/400) of patients, auto-HCT for 56.7% (227/400). Allo-HCT was associated with an average of 1.01 fewer infection episodes per 100 admission days (95% CI 0.62–1.40, P<0.001) compared with auto-HCT. In allo-HCT, the total exposure to all antimicrobials was higher (+24.8 days of therapy [DOT]/100 admission days, P<0.001), as was exposure to ciprofloxacin (+40.5 DOT/100 admission days, P<0.001). In contrast, exposure to meropenem (−4.5 DOT/100 admission days, P=0.02), piperacillin/tazobactam (−5.2 DOT/100 admission days, P<0.001), aminoglycosides (−4.5 DOT/100 admission days, P<0.001), glycopeptides (−6.4 DOT/100 admission days, P<0.001), was reduced. Enterobacteriaceae isolated during allo-HCT were more resistant to ciprofloxacin (65.5%, 19/29 versus 6.1%, 2/33, P<0.001), ceftriaxone (65.5%, 19/29 versus 9.1%, 3/33, P<0.001), and other antimicrobial classes. Vancomycin-resistant enterococci were more common in allo-HCT recipients (11%, 19/173 versus 0.9%, 2/227, P<0.001). Inpatient mortality during allo- and auto-HCT was 9.8% (17/173) and 0.4% (1/227) respectively (P<0.001). An invasive bacterial infection was documented in 31.3% (125/400) of cases. Allo-HCT patients were more likely to have an invasive Gram-positive bacterial infection (23.1% versus 12.8%, P=0.01), while a difference was not observed for invasive Gram-negative bacterial infections (19.7% versus 18.5%, P=0.77). Among auto-HSCT recipients, patients with germ cell tumours had the highest probability (P for trend 0.03) of recording an invasive bacterial infection (12/23, 52.2%, 95% CI 31.3–74) compared with other indication for auto-HCT. Conclusions Ciprofloxacin prophylaxis in allo-HCT was associated with fewer infection episodes and reduced exposure to treatment antimicrobials. Mortality in auto-HCT remained low. A significant burden of antimicrobial resistance was detected in allo-HCT recipients. HCT recipients due to germ cell tumours, not receiving ciprofloxacin prophylaxis, recorded the highest incidence of invasive bacterial infections and represent a possible target group for this intervention.