 In connection with the larger Mennonite denomination, a “Confession of Faith in a Mennonite Perspective (1995) was accepted, along with membership, in the year 2000, in a joint “Mennonite Church USA.”

Franconia Conference has had trouble in recent decades dealing with issues of sexual orientation and gender identity, with one of its congregations fully embracing lesbian, gay, bisexual, and transgender persons.The conference removed Germantown Mennonite Church from its membership in 1997, and in 2009 began the process of removing Alpha Mennonite Church of New Jersey for standing with its openly gay pastor.Alpha eventually changed pastors and remains with the conference.