The 45-year-old was praised by the Bishop of Stafford as bosses at the Bet365 Stadium announced he is replacing Gary Rowett.
Rt Rev Geoff Annas was quoted by the Daily Telegraph as saying: “It’s so impressive that Nathan is able to talk openly and honestly about his faith and it’s particularly great that he has found strength from this during times of adversity”.
Jones, who regularly attends church and has Christian-themed tattoos, has described how God has kept him “grounded” and helped him persevere in the face of temptation.
During an interview with The Football League Paper in 2006, he also said: “Through the hard times I’ve always had the stability of the Lord in my life, and my family background has kept me on the straight and narrow.
“I believe everything is God’s will.”
Jones leaves Luton Town after three years at the reins of the club. He powered The Hatters to promotion from League Two last season.
The Potters, who are currently 14th in the Championship table, say they have struck a compensation package with Luton Town.
Last year, Stoke City were relegated from the Premier League.
Bishop Geoff added: “We would certainly pray for promotion should he ask us too.”
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Nathan Jones, the new manager of Stoke City Football Club, has been extolled by his local Church of England bishop for talking “openly and honestly” about his Christian faith.