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Introduction Allogeneic haematopoietic stem cell transplantation (allo-HSCT) is a highly complex procedure involving intensive conditioning regimens, immunosuppressive therapy and extensive supportive care.Objective To assess the impact of a comprehensive pharmaceutical care programme on medication adherence in allo-HSCT patients. Early survival and clinical and patient-reported outcomes will also be explored.Methods and analysis Prospective interventional study with a historical control group. The primary outcome is medication adherence. Secondary outcomes will include the incidence of grade I–IV acute graft-versus-host disease (aGVHD); acute graft-versus-host disease-free, relapse-free survival (aGRFS); relapse-free survival (RFS) and overall survival (OS) by day+100; hospital readmissions; acute renal and liver failure; engraftment time; drug-related problems (DRPs); pharmaceutical interventions and patient-reported outcomes. Patients will be enrolled over a 12-month period in the intervention group and compared with a historical cohort of patients undergoing allo-HSCT. The intervention will include a structured pharmacist-led programme including: (1) a pre-admission interview, (2) in-hospital follow-up with daily medication review and DRP identification, (3) patient education at discharge and (4) post-transplant pharmaceutical follow-up to day+100.Ethics and dissemination The study protocol was approved by the hospital Clinical Research Ethics Committee (CEIm code: 245/23). Written informed consent will be obtained from all participants. Data will be handled in accordance with the EU General Data Protection Regulation (2016/679) and Spanish Organic Law 3/2018 on Data Protection and Digital Rights.