Treatment. Treating bacterial vaginosis will require the use of a medication. Some women first confuse it for a yeast infection, opting for self-treatment from home. In the event that this is ineffective, a doctor may prescribe one of several medications. Metronidazole comes in both a pill and topic gel form. While effective, it has also been shown to cause abdominal pain and/or nausea and should not be taken with alcohol. Tinidazole is also taken orally and has the potential to leave a woman with an upset stomach. Clindamycin is another cream that can be inserted into the vagina in order to eliminate the excessive bad bacteria. Treatment is typically only necessary for the infected woman- not all of her partners.