In his address at his enthronement as the 13th Archbishop John challenged churches to "rehabilitate and refresh" how they explained the Gospel message, particularly to young people.
He explained that being a Christian was not about just going to church.
"We are not always seen for the good which we do, or for the just causes which we support or further, or for the justice and truth for which we call," he said.
About 600 people from all over Wales filled Brecon Cathedral for the enthronement of Archbishop John on Saturday afternoon. The service began with a long procession which included clergy, visiting bishops, diocesan legal officers, ecumenical and interfaith guests and representatives of academic institutions.
During the service, the Archbishop made his declaration and oath on the historic William Morgan Bible, specially brought from St Asaph Cathedral for the occasion, and he was placed in the Archiepiscopal chair (or throne) by the Bishop of Bangor, the Senior Bishop, who then presented him to the congregation.
In his address, the Archbishop called on churches to make New Year Resolutions to help people grasp what their faith was really about.
He said: "Let churches resolve to face down the caricature of being an institution, focussed on simply surviving and being against things.
"Let churches and their charities, resolve to proudly affirm caring, loving and open-handed initiatives which, often in partnership with others, they are already taking; supporting and affirming needy communities and people.
"Often the work goes unseen, as does a remarkable amount ordinary but supportive community
The Archbishop said he had an 'active and deep concern' for witness to young people who were not associating the Gospel message with their own strong sense of right.
He said, "So many of them so evidently have a deep and clearly-articulated sense of moral right.
"They are keenly aware of the need for social and economic justice, the stewardship of creation, and equality of opportunity; they are equally aware of the need for a society free from any form of prejudice rooted in anything which is part of the individual identity, gender, race, origin, religion or orientation of anyone."
Archbishop John also urged everyone to speak up against injustice and oppression.
He said, "Beyond the churches and religion, can we not all simply resolve, in our increasingly divided, bewildered and uneven society, to be clothed with goodness, to call to account and encourage the reform of individuals and entities which deliberately or by stealth, neglect and carelessness collude in oppressing minorities, burdening the poor and robbing individuals of their dignity?"
