Abstract Objectives Compare home health care (HHC) with self-governing and conventional team structure regarding self-reported low back pain (LBP) and work-related factors. Methods A natural experiment was assessed using a cross-sectional design. Primary outcome was LBP intensity; secondary outcomes included LBP duration and work limitations as well as intensity, duration and work limitations of neck/shoulder pain, stress, productivity, influence at work, meaning at work, sickness absence, interpersonal collaboration, and variation in physical behaviour. Home health care (HHC) workers in the self-governing teams were surveyed about their appraisal of the self-governing structure. Data were collected through a questionnaire, except for physical behaviour, which was obtained via accelerometry. Differences between groups were analyzed using t-tests. Results From 10 HHC-teams across four municipalities, 125 HHC-workers completed the questionnaire (self-governing n = 60; conventional n = 65). LBP intensity was similar among HHC-workers in the two team structures (self-governing = 4.1; conventional = 4.0, 0–10 scale). Self-governing teams experienced significantly higher levels of (i) meaning at work (5.8 points, 0-100 scale), (ii) improved collaboration with manager (7.5 points, 0-100 scale) and (iii) improved collaboration with needs assessors (11.9 points, 0-100 scale) compared to conventional teams. No significant differences were found in the other outcomes. Conclusions The higher scores for self-governing teams in meaning at work, collaboration with manager and collaboration with needs assessors are positive. The lack of a lower report in LBP and neck/shoulder pain calls for more focused efforts to enhance HHC-workers’ health in addition to the reorganization into the self-governing structure.