Caution to PCOS Women: Metformin May Lead to Vitamin B12 Problems http://www.ovarian-cysts-pcos.com/glucophage-... Women with PCOS who take metformin (Glucophage) for a long time are at risk for vitamin B12 insufficiency.Metformin interferes with your ability to absorb vitamin B12 from your food.B12 is essential to the proper function of every cell in your body. There is also a link between B12 insufficiency and cardiovascular disease, which is a risk of PCOS.