I take magnesium twice a day, but with calcium which I need because I tend to be low. I take magnesium bis-glycinate in the morning on an empty stomach about 30mins to an hour after my glutamine, and about 30 mins before my light morning snack. I take my last dose right before bed. So far, I have not had any worsening of my digestion with this system. In fact, due to other things I am actually improving. If you have to take an afternoon dose, I would suggest taking it about 2 hours after your lunch so that it will not interfere too much with your digestion or absorption as that meal should be the largest meal of the day.