A magnetic flowmeter flowtube assembly includes a conduit with a first end and a second end. A first neck flange is coupled to the first end of the conduit and has an inside diameter with a first notch extending radially outwardly therefrom. A second neck flange is coupled to the second end and has an inside diameter with a second notch extending radially outwardly therefrom. A fluoropolymer liner is disposed within and extends through the first neck flange, the conduit and the second neck flange. A pair of electrodes is mounted relative to the liner to measure a voltage induced within a process fluid flowing through the liner. A first spring-energized seal ring is disposed in the first notch and a second spring-energized seal ring disposed in the second notch. A method of sealing a magnetic flowmeter having a fluoropolymer liner is also provided.