Many common medications are linked with nutrient deficiencies. Such as: Birth control pills can cause Folate deficiency. Antacids can cause Vitamin B12 deficiency. Metformin can cause Vitamin B12 deficiency. Anti-seizure drugs can cause Folate and Vitamin D deficiency. PPIs can cause Vitamin B12 and Magnesium deficiency. Corticosteroids can cause Calcium and Vitamin D deficiency.