We set out to determine whether a minimally invasive approach for one-level instrumented posterior lumbar interbody fusion reduced undesirable changes in the multifidus muscle, compared to a conventional open approach. We also investigated associations between muscle injury during surgery (creatinine kinase levels), clinical outcome and changes in the multifidus at follow-up. We studied 59 patients treated by one team of surgeons at a single institution (minimally invasive approach in 28 and conventional open approach in 31, voluntarily chosen by patients). More than 1 year postoperatively, all the patients were followed up with the visual analogue scale (VAS) and Oswestry disability index (ODI), and 16 patients from each group were evaluated using MRI. This enabled the cross-sectional area (CSA) of lean multifidus muscle, and the T2 signal intensity ratio of multifidus to psoas muscle, to be compared at the operative and adjacent levels. The minimally invasive group had less postoperative back pain (P < 0.001) and lower postoperative ODI scores (P = 0.001). Multifidus atrophy was less in the minimally invasive group (P < 0.001), with mean reductions in CSA of 12.2% at the operative and 8.5% at the adjacent levels, compared to 36.8% and 29.3% in the conventional open group. The increase in the multifidus:psoas T2 signal intensity ratio was similarly less marked in the minimally invasive group where values increased by 10.6% at the operative and 8.3% at the adjacent levels, compared to 34.4 and 22.7% in the conventional open group (P < 0.001). These changes in multifidus CSA and T2 signal intensity ratio were significantly correlated with postoperative creatinine kinase levels, VAS scores and ODI scores (P < 0.01). The minimally invasive approach caused less change in multifidus, less postoperative back pain and functional disability than conventional open approach. Muscle damage during surgery was significantly correlated with long-term multifidus muscle atrophy and fatty infiltration. Furthermore these degenerative changes of multifidus were also significantly correlated with long-term clinical outcome.