Does long term methadone use affect your liver?

Probably not. Liver dysfunction is not listed as a serious or less serious effect of Methadone use. One should always be careful with long term use of medications and have routine follow up and lab studies. Many medications used with Methadone certainly could cause liver dysfunction. Methadone is a very serious medication. Take its use and follow up very seriously.
Metabolized in liver. Methadone like many drugs is metabolized in the liver. Long term use at medically accepted dose should not cause liver damage. Pre-existing liver failure is a contraindication to methadone.