Introduction Low back pain (LBP) is the leading cause of disability and a major public health concern. Literature generally supports the effectiveness of exercise therapy for the treatment of chronic non-specific LBP, but there have only been modest effects. Considerable evidence suggests a link between lumbar multifidus degenerative changes and functional deficits. Recent preliminary evidence suggests that motor control and targeted lumbar extensor strength training may lead to hypertrophy and reduce fatty infiltration, however the optimal exercise intervention for reversing these changes is unknown. Objectives To study the effects of combined motor control and extensor strengthening on multifidus morphology and function, and to determine how physiological changes relate to pain, function, and psychological factors. Participants The study included 25 participants aged 18 to 65 with moderate-to-severe chronic non-specific LBP. Intervention Participants completed a 12-week supervised motor control and isolated lumbar extension intervention at a frequency of two times per week. Measures Primary: multifidus morphology Secondary: multifidus function, lumbar extensor strength, pain, self-reported outcomes Results There were significant increases in the paraspinal CSA at L4-5 and L5-S1 between all timepoints and significant decreases in %fat fraction of multifidus and erector spinae at L5-S1 between baseline and both 6 and 12-weeks. There were significant increases in multifidus thickness and lumbar extensor strength between all timepoints. Conclusion Our results suggest that an intervention combining motor control and isolated lumbar extensor training has the potential to be successful in improving a large variety of outcomes, both physiological and clinical, in patients with chronic LBP.