Abstract Background The quality of provided health care may be an important source of variation in rehabilitation outcomes, increasing the interest in associations between quality indicators (QIs) and improved patient outcomes. Therefore, we examined the associations between the quality of rehabilitation processes and subsequent clinical outcomes among patients with rheumatic and musculoskeletal diseases (RMDs). Methods In this multicentre prospective cohort study, adults with RMDs undergoing multidisciplinary rehabilitation at eight participating centres reported the quality of rehabilitation after 2 months and outcomes after 2, 7, and 12 months. We measured perceived quality of rehabilitation by 11 process indicators that cover the domains of initial assessments, patient participation and individual goal-setting, and individual follow-up and coordination across levels of health care. The patients responded “yes” or “no” to each indicator. Scores were calculated as pass rates (PRs) from 0 to 100% (best score). Clinical outcomes were goal attainment (Patient-Specific Functional Scale), physical function (30 s sit-to-stand test), and health-related quality of life (EuroQoL 5D-5L). Associations between patient-reported quality of care and each outcome measure at 7 months was analysed by linear mixed models. Results A total of 293 patients were enrolled in this study (mean age 52 years, 76% female). Primary diagnoses were inflammatory rheumatic disease (64%), fibromyalgia syndrome (18%), unspecific neck, shoulder, or low back pain (8%), connective tissue disease (6%), and osteoarthritis (4%). The overall median PR for the process indicators was 73% (range 11–100%). The PR was lowest (median 40%) for individual follow-up and coordination across levels of care. The mixed model analyses showed that higher PRs for the process indicators were not associated with improved goal attainment or improved physical function or improved health-related quality of life. Conclusions The quality of rehabilitation processes was not associated with important clinical outcomes. An implication of this is that measuring only the outcome dimension of quality may result in incomplete evaluation and monitoring of the quality of care, and we suggest using information from both the structure, process, and outcome dimensions to draw inferences about the quality, and plan future quality initiatives in the field of complex rehabilitation. Trial registration The study is part of the larger BRIDGE trial (ClinicalTrials.gov NCT03102814).