BackgroundChronic low back pain (CLBP) is a highly prevalent disease with poorly understood underlying mechanisms. In particular, altered trunk muscle coordination in response to specific trunk tasks remains largely unknown.MethodsWe investigated the muscle synergies during 11 trunk movement and stability tasks in 15 healthy individuals (8 females and 7 males, aged 21. 3 (20.1–22.8) ± 0.6 years) and in 15 CLBP participants (8 females and 7 males, aged 20. 9 (20.2–22.6) ± 0.7 years) by recording the surface electromyographic activities of 12 back and abdominal muscles (six muscles unilaterally). Non-negative matrix factorization was performed to extract the muscle synergies.ResultsWe found six trunk muscle synergies and temporal patterns in both groups. The high similarity of the trunk synergies and temporal patterns in the groups suggests that both groups share the common feature of the trunk coordination strategy. We also found that trunk synergies related to the lumbar erector spinae showed lower variability in the CLBP group. This may reflect the impaired back muscles that reshape the trunk synergies in the fixed structure of CLBP. Furthermore, the higher variability of trunk synergies in the other muscle regions such as in the latissimus dorsi and oblique externus, which were activated in trunk stability tasks in the CLBP group, represented more individual motor strategies when the trunk tasks were highly demanding.ConclusionOur work provides the first demonstration that individual modular organization is fine-tuned while preserving the overall structures of trunk synergies and temporal patterns in the presence of persistent CLBP.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12984-023-01190-z.