Empiric antibiotic treatment for bloodstream infection (BSI) after haematopoietic cell transplantation (HCT) in the era of antimicrobial resistance is challenging. We conducted a nested project in the Swiss Transplant Cohort Study 09/2009 to 10/2018 assessing BSI incidence, pathogen distribution and antimicrobial resistance. Cox proportional hazards models were fitted to detect factors associated with BSI and outcome. We included 1 364 adults (61.1% male) receiving 1 432 HCTs complicated by 676 BSIs in 451 (33%) patients. Cumulative incidence of BSI was 20.5% (95%CI 18.4 – 22.7) until day 100 after the first HCT. Gram-positive pathogens, mostly coagulase-negative staphylococci, dominated (454, 58.1%). Production of extended-spectrum beta-lactamases and quinolone-resistance were observed in 41/195 (21%) and 81/195 (41.5%) of Enterobacterales, respectively. Carbapenem-resistance was documented in 10/49 (20.4%) of Pseudomonas aeruginosa isolates. Multivariable cox regression analysis within the first-year post-transplant identified male gender, comorbidities, myeloablative regimen, acute graft-versus-host disease grade III/IV and haematological progression/relapse after HCT as independent risk factors for BSI. One-year mortality was 26.6% with BSI modeled as a time-dependent covariable independent risk factor for mortality. To conclude, BSI remains a frequent complication after HCT, with stable rates of antibiotic resistance in BSI-causing pathogens in Switzerland. BSI was a major contributor to mortality.