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Low back pain (LBP), a globally widespread and persistent musculoskeletal disorder, benefits from exercise therapy. However, it remains unclear which type leads to greater changes in paraspinal muscle health. This study aimed to (1) compare the effects of a combined motor control and isolated lumbar extension exercise (MC+ILEX) versus a general exercise (GE) intervention on paraspinal muscle morphology, composition, and function, and (2) examine whether alterations in paraspinal muscle health were correlated with improvements in pain, function, and quality of life. Fifty participants with chronic LBP were randomly assigned to each group and underwent a 12-week supervised intervention program. Magnetic resonance imaging and ultrasound assessments were acquired at baseline, 6 and 12 weeks to examine the impact of each intervention on erector spinae (ES) and multifidus (MF) muscle size (cross-sectional area, CSA), composition, and function at L4-L5 and L5-S1. Self-reported questionnaires were also acquired to assess participant-oriented outcomes. Our findings indicated that the MC+ILEX group demonstrated greater improvements in MF and ES CSA, along with MF thickness at both levels (all p < 0.01). Both groups significantly improved in pain, function, and quality of life. This study provided preliminary results suggesting that an MC+ILEX intervention may improve paraspinal morphology while decreasing pain and disability.