The study investigated the causal associations between abdominal obesity, dietary habits and intervertebral disc degeneration (IVDD) using two-way two-seed Mendelian randomization with data from the IEU OpenGWAS and FinnGen databases (41,669 cases, 294,770 controls). Genetically predicted waist circumference (WC) and abdominal subcutaneous adipose tissue (ASAT) were positively associated with IVDD (WC: OR = 1.209, 95% CI: 1.091–1.34; ASAT: OR = 1.149–1.535), while BMI, hip circumference (HC) and BMI-adjusted waist-to-hip ratio (WHR-BMI) showed no association. A higher intake of mushrooms, porridge and white fish increased the risk of IVDD, while apples, cereal bars, Danish pastries, espresso, lobster/crab and other fruits had a protective effect. A clinical study of 512 IVDD patients and 512 controls confirmed higher WC (OR = 1.32, 95% CI: 1.10–1.58) and frequent mushroom consumption (OR = 1.28, 95% CI: 1.05–1.56) as risk factors, while higher fruit intake was protective (OR = 0.76). The results support a causative role of WC and AST in IVDD independent of general obesity and emphasize the influence of specific dietary habits.