Osteopenia and metabolic bone disease (MBD) are common in captive chelonians and are most often attributable to inadequate ultraviolet B (UVB) exposure and dietary calcium–vitamin D imbalance. Clinical signs are frequently nonspecific and may coexist with reproductive, gastrointestinal, or urinary disorders that complicate diagnosis and management. A female desert tortoise (Gopherus agassizii) presented with prolonged brumation and progressive anorexia. Survey radiography revealed four concurrent abnormalities: (1) a thin-walled mineralized left coelomic structure consistent with a retained egg; (2) segmental gas distension with granular radiopaque material compatible with partial gastrointestinal obstruction; (3) a multilayered mineral opacity within the mid-coelom consistent with a cystic calculus; and (4) generalized decreased bone density with a pathologic fracture of the proximal right fibula, confirming osteopenia. The findings supported a multifactorial etiology in which nutritional/calcium–vitamin D deficiency and suboptimal husbandry were compounded by reproductive and obstructive gastrointestinal pathology. Treatment prioritized husbandry correction (optimized UVB lighting and photoperiod), dietary calcium and vitamin D supplementation, analgesia and supportive fluid/nutritional care, and targeted management of the obstructive and reproductive lesions. Owner education and close follow-up were instituted. This case highlights the diagnostic value of plain radiography in chelonians with vague systemic signs and illustrates how inadequate husbandry can precipitate reproductive, gastrointestinal, and urinary complications that exacerbate skeletal demineralization. Preventive measures — evidence-based UVB provisioning, balanced dietary calcium/phosphorus, and routine imaging of at-risk animals — are essential to reduce MBD morbidity in Gopherus agassizii.