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Background: Chronic low back pain (CLBP) patients present with morphological and functional deficits to the lumbar multifidus. Electromyostimulation (EMS) can be used to improve activation and strength in atrophied skeletal muscle, but its effect on multifidus morphology and function in CLBP patients is understudied. The aims of this study were to compare the effect of two EMS protocols on lumbar multifidus morphology, function, and patient-reported outcomes. Methods: Two-arm randomized control trial (RCT). Individuals with CLBP were randomized to receive either the 'phasic' or 'combined' muscle therapy protocol with the StimaWELL 120MTRS, a medium-frequency EMS device. T-tests and non-parametric equivalents were used to assess change in imaging-based outcomes, and a repeated-measures ANOVA was used for patient-reported outcomes. Results: Apart from a significant within-group decrease in fatty infiltration at left L5-S1 in the combined group (MD = -1.51, 95% CI = -2.79, -0.23, p = 0.024), results revealed no significant within- or between-group changes to multifidus morphology or function. Pairwise comparisons revealed that both groups experienced significant improvements in multiple pain outcome measures, with a significant group*time effect for LBP with sitting (p = 0.019) and pain interference (p = 0.032) in favor of the phasic group. Additionally, there were significant improvements in the phasic group in disability, pain interference, and pain catastrophizing (all p < 0.01). Conclusions: A 10-week EMS intervention produced no between-group differences in multifidus muscle morphology or function. Participants in both groups experienced significant improvements in a variety of patient-reported outcomes.