The Tigers reached the Vanarama National League North top seven against all odds after a great end to the season.
But manager Steve King declared he needed a new challenge after they fell to Eliminator defeat - and after the club decided to return to part-time status.
Former England keeper Flowers says he knows it will take a lot to put together another promotion challenge.
But after getting the job he says he can’t wait for what’s ahead.
He told the club’s website: “I’m very proud and pleased to be joining Gloucester City.
“Patrick was very candid regarding the model for next season - it’s a rough, rugged league and we want to be as competitive as possible.
“We’ll need to box clever in the transfer market, and bring in some players who can form a tight knit squad who the fans will warm to.
“The club were unlucky in the play-offs after a very good season and as part of the recruitment process I’ll naturally be speaking to last season’s squad.”