Flint, pictured, accepted the role on a permanent basis on Thursday having steered the club to safety with two games to go during a nine-game tenure as caretaker boss following the departure of Garry Kimble at the end of February.
Town did it the hard way again at Spa Road on Saturday, securing a 19th placed finish in the end after twice coming from behind to beat Cheshunt 3-2 and finish on a high thanks to Scott Kemp's last minute goal.
Town's officials say Flint, assistant-manager James Robinson and coach Curtis Whyte agreed to stay on after winning unanimous backing from the club's board for securing the four wins and a draw that kept them up.
Witham Town chairman Mark Nicholls told the Braintree & Witham Times: "We had a meeting and decided to offer the job to Adam and I'm delighted to say that he has accepted it on a permanent basis for next season.
"He did what the club asked him to do in keeping us up and the disciplinary record in achieving that has been superb. It was done with basically the same group of players that were here when Garry left.
"People may turn round and say 'are you sure?' but why wouldn't we? Adam is a local lad who wants to make his mark and he deserves his chance. It was definitely the right decision to ask him to take over as caretaker and he's got the whole Board's backing for the permanent position."
He added: "We have announced it now because Adam will now have a full pre-season to prepare for next season and we see it as a positive move for Adam and for the club. Everyone has been full of praise and he has everyone's backing."
Image courtesy of Witham Town
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