Mar 10, - But, most commonly, the cause isn't an infection at all. An imbalance of the various kinds of bacteria found in the vagina can cause discomfort and odor as well. This imbalance is known as bacterial vaginosis. For those past menopause who experience vaginal odor, lack of estrogen could be the cause. May 21, - Not using scented or flavored products in or around the vagina. Hormonal changes during menopause may alter the scent of the vagina, and.