Patients with neuroendocrine tumors of gastro-entero-pancreatic origin (GEP-NET) experience changes in fat and muscle composition. Dual-energy X-ray absorptiometry (DXA) and bioelectrical impedance analysis (BIA) are currently used to analyze body composition. Changes thereof could indicate cancer progression or response to treatment. This study examines the correlation between CT-based (computed tomography) body composition analysis (BCA) and DXA or BIA measurement. 74 GEP-NET-patients received whole-body [68Ga]-DOTATOC-PET/CT, BIA, and DXA-scans. BCA was performed based on the non-contrast-enhanced, 5 mm, whole-body-CT images. BCA from CT shows a strong correlation between body fat ratio with DXA (r = 0.95, ρC = 0.83) and BIA (r = 0.92, ρC = 0.76) and between skeletal muscle ratio with BIA: r = 0.81, ρC = 0.49. The deep learning-network achieves highly accurate results (mean Sørensen-Dice-score 0.93). Using BCA on routine Positron emission tomography/CT-scans to monitor patients’ body composition in the diagnostic workflow can reduce additional exams whilst substantially amplifying measurement in slower progressing cancers such as GEP-NET.