Background: Chronic non-specific low back pain (CNSLBP) is often associated with morphological changes in the lumbar multifidus muscle (LMF), such as reduced cross-sectional area (CSA) and increased fat infiltration, compromising spinal stability and function. Core stabilization exercises aim to enhance neuromuscular control by targeting deep trunk muscles. However, few randomized trials have investigated their effects on MRI-based muscle morphology and clinical outcomes. This study aimed to compare the effects of an 8-week core stabilization exercise program versus conventional physiotherapy on LMF morphology, pain intensity, disability, and core stability in individuals with CNSLBP. Methods: In this two-arm, parallel-group randomized controlled trial, 36 individuals with CNSLBP (> 3 months) were randomized to a Core Exercise Group (CEG, n = 18) or a Conventional Physiotherapy Group (CPG, n = 18). The 8-week intervention included a 4-week supervised clinical phase and a 4-week home-based phase. The primary outcome was the CSA of the LMF, as this parameter was used for the sample size calculation. Secondary outcomes included LMF fat infiltration (Goutallier grade), pain intensity (visual analog scale), functional disability (Oswestry Disability Index), and core stability (Sahrmann test). Assessments were conducted at baseline and post-intervention. We analyzed within-group change, between-group differences, and group × time interactions using mixed ANOVA; when assumptions were violated, we used non-parametric alternatives (including ART ANOVA). Effect sizes were reported. Results: Thirty-one participants completed the trial (CEG, n = 15; CPG, n = 16). Both groups showed significant improvements in clinical and functional outcomes (p < 0.05). The CEG additionally demonstrated greater CSA increases—especially at L3–L5 levels (p < 0.01)—and more notable reductions in fat infiltration (p < 0.05). Activity-related pain decreased by 4.4 points in the CEG versus 1.8 points in the CPG (p < 0.001). Functional disability improved by 31 points in the CEG compared to 10 points in the CPG (p < 0.001). Core stability increased to a median Sahrmann test level of 4 in the CEG versus 3 in the CPG (p < 0.001). Conclusions: Core stabilization exercises yielded superior improvements in LMF morphology, pain relief, functional recovery, and trunk control compared to conventional physiotherapy in individuals with CNSLBP. These findings support the integration of core-focused rehabilitation strategies into standard clinical practice for CNSLBP. Trial registration: ClinicalTrials.gov Identifier: NCT05302349, protocol ID: 2022–695, registered on March 21, 2022.