The long-term usage of omeprazole includes hypomagnesemia, Increased risk of infection, vitamin B 12 deficiency, iron deficiency anemia, osteoporosis, and mental disorders.
Joint pain is a rare but serious side effect of omeprazole due to subacute cutaneous lupus erythematosus which is is commonly resolved a few days after stopping omeprazole administration.
Omeprazole is commonly prescribed once daily. It is better to be taken at the morning before breakfast. Read more about administration of omeprazole