Low back pain is a common health problem. In this study, we investigated the effects of yoga, physical therapy (PT), and home exercise (HE) on pain perception, function, stress, and quality of life in chronic low back pain (cLBP). We randomly assigned 54 participants to three distinct treatment groups: (a) a physical therapy group (PT) who received spinal stabilization exercises (SSE) combined with local heat and transcutaneous electrical stimulation; (b) a home exercise group (HE) who received SSE as part of the home program; and (c) a yoga group who received yoga exercises. The primary outcome measures were a Visual Analog Scale (VAS) for measuring pain, and the Oswestry Disability Index (ODI) to measure function. Secondary outcome measures were the Tampa Kinesiophobia Scale (TKS), Central Sensitization Inventory (CSI), pain sensitivity (L3 and deltoid R/L PPTs), Spielberger State-Trait Anxiety Inventory (STAI), plasma cortisol and DHEA-S levels, Transversus Abdominis (TrA) muscle activation, and the Nottingham Health Profile (NHP). Assessments were conducted before and after a six-week intervention period. All three groups demonstrated improvements in pain on the VAS, function on the ODI, pain sensitivity on the L3 and deltoid R/L PPTs, CSI, anxiety on the STAI, TrA muscle activation, and quality of life on the NHP (p < .05). The PT group exhibited a more pronounced improvement on the ODI score (p < .05) than the other groups. Cortisol levels only decreased in the PT group (p < .05). The exercises did not impact DHEA-S and NHP-S parameters. Thus, all interventions resulted in decreased stress, pain intensity, pain sensitivity, central sensitization, and improved function and quality of life; there was no singularly superior approach between interventions. These findings will aid in tailoring treatment programs for managing cLBP according to individual needs.