Patients undergoing malabsorptive weight-loss procedures are at increased risk of calcium and vitamin D deficiency. Thyroidectomy carries the risk of both immediate and long-term hypocalcemia. Here we describe a patient who underwent Roux-en-Y gastric bypass (RYGB) and subsequent near-total thyroidectomy and then developed refractory hypocalcemia. Serum calcium reached a nadir of 6.1 mg/dl despite aggressive therapy with oral and IV calcium, calcitriol (1,25(OH)₂D₃), and IV magnesium sulfate. One year later, the patient has permanent hypoparathyroidism and requires very high doses of calcium, vitamin D, and calcitriol to prevent symptomatic hypocalcemia. Providers should be aware that malabsorption of calcium and vitamin D after RYGB may complicate patient management after thyroidectomy.