Vertebral end-plate changes and paraspinal muscles are recently getting much more attention, since they could be associated with intervertebral disc degeneration (IVDD) and low back pain (LBP). Even though obesity is known as a risk factor for LBP, the role of obesity in the process of LBP is still controversial. In this study, we aimed to identify whether increased body mass index (BMI) was associated with IVDD, vertebral end-plate changes and paraspinal muscle quality. Consecutive women and men, aged between 20 and 50 years, presented with chronic LBP to the outpatient clinics were included. Patients were evaluated in terms of IVDD, vertebral end-plate changes, fatty infiltration in the paraspinal muscles at all lumbar levels on magnetic resonance imaging. Severe IVDD was more common in obese patients than in non-obese patients (73.5% vs. 50.4%, p = 0.017). When we compared the groups level by level, the significant difference for severe IVDD was present only at L4-L5 disc level (50% vs. 27.4%, p = 0.013). There was a higher trend of harboring Modic change at any lumbar level in obese patients, significantly in women (35.9% vs. 16.4%, p = 0.026). More severe fatty infiltration in the paraspinal muscles was seen at upper lumbar levels of the obese patients, particularly in women. Patients with higher BMI and suffering from LBP, had more fatty infiltration in the paraspinal muscles at the upper lumbar levels, more severe IVDD, and Modic changes at the lower lumbar levels; particularly women.