Immune-mediated rheumatologic and musculoskeletal diseases (RMDs) comprise a heterogeneous group of systemic conditions that affect the connective tissues of the musculoskeletal system and internal organs. Immune-mediated RMDs are driven by chronic autoimmune responses and typically require continuous or repeated administration of immunosuppressive or biologic disease-modifying drugs. Although generally effective, these therapies can cause both short- and long-term side effects and may fail to control the disease with risk of irreversible tissue damage. For such patients, haematopoietic stem cell transplantation (HSCT) has been successfully employed over the past 30 years, but this procedure requires caution due to significant side effects. To address these aspects, updated recommendations for the use of HSCT in RMDs have been developed in collaboration with an international expert panel from the European Society for Blood and Marrow Transplantation (EBMT). The panel reviewed all available evidence regarding HSCT application since 2004. Based on this review, EBMT expert-based consensus recommendations were formulated to guide best practices and ensure high-quality patient care. These recommendations include detailed indications, contraindications, and cautionary notes specific to each RMD, along with comprehensive protocols for diagnostic work-up. They are intended to support clinicians, scientists, patients, and caregivers in the field of RMDs.