An inspired second half performance means the Blues are up and running for the 2014-15 season.
Sean McConville was the star of the show, scoring twice and creating another for Chris Iwelumo to complete an excellent comeback.
Braintree took the lead through a Kenny Davis penalty but could have been three or four goals to the good at half time and that profligacy proved all too costly.
Steve Burr might have had some harsh words for his side in the break and if that's the case then it did the trick because the Blues were unrecognisable in the second half.
There are still things to work on but this result will provide further belief that this team can make a real improvement on last season.
Two defeats had not been the start the Blues had wanted, but given both Barnet and Forest Green Rovers are expected to be in the promotion mix, it was perhaps not unexpected.
It had been a strange old week for Burr and his squad: dismissed as no-hopers after the Barnet hammering before restoring belief with a much-improved showing at Forest Green Rovers on Tuesday.
Burr made two changes from that game, bringing in John Disney for Danny Taylor and replacing Craig Hobson with Iwelumo.
Ben Heneghan, a 20-year-old centre back signed the previous afternoon, made the bench along with Wayne Riley, who missed the first two games through suspension.
Braintree are one of a few part-time clubs remaining in the Vanarama Conference but that didn't stop them securing a top-six finish last season.
Manager Alan Devonshire - whose dad Les spent the 1950-51 season with the Blues - has put together a team that works hard and battles to the end, and that has been rewarded with results.
Braintree went down 1-0 at Macclesfield Town on the opening afternoon but responded with a 3-0 win at home to Dover Athletic midweek, and Devonshire named the same starting side.
Slow starts have hampered the Blues in both games this season and the home side almost took the lead inside the first minute here.
Chez Issac exposed some slack defending to power in a shot from 10 yards but keeper Freddy Hall turned the ball behind with an excellent one-handed save.
Hall was beaten a minute later when Sean Marks stole in to meet Dan Sparkes' corner but the crossbar came to the Blues rescue before Hall made another stop down to his right.
Chester came through the onslaught unscathed and on five minutes John Rooney forced Iron keeper Nick Hamann into a save with a well-hit free kick from 25 yards.
Things soon settled down and both teams were content to feel each other out for the next 15 minutes or so with no real chances.
But the home side were handed the opening goal on 23 minutes when a deep free kick was pumped into the box and the ball struck Disney on the arm.
Referee John Brooks pointed to the spot and booked the fullback before Iron captain Kenny Davis stepped up to convert.
Chester didn't deserve to be behind and the response to conceding was good. Hamann pushed the ball from under the crossbar after Craig Mahon flicked on Peter Winn's corner and Kieran Charnock couldn't quite connect with a wicked Rooney free kick.
Although the Blues moved the ball well forward enough, the lack of threat and some nervous moments were a concern.
Matty Brown made a last-ditch tackle to block Dan Walker's shot after Charnock had slipped on 38 minutes and Marks missed the target with a free header after the offside trap backfired.
Walker had another chance seconds before half time but screwed wide with the defence all at sea and the 1-0 score meant the Blues were still in the contest despite the hosts having chances to put the game to bed.
Burr introduced Heneghan for Disney during the break and the start to the second period suggested there had been some strong words in his teamtalk.
Rooney hit the post on 47 minutes after bringing the ball under control with a touch of class and the equaliser came a minute later when Sean McConville picked up a loose ball, turned and opened up his body before firing across Hamann and into the bottom corner.
Iwelumo then fired over from 15 yards after Winn's cross had reached the back post as the home side were slow out of the blocks.
Braintree steadied the ship and created a chance on 56 minutes when Hall grabbed Mitch Brundle's overhead effort from Sparkes' free kick but the Blues looked a different side.
McConville was a real menace and created the second for Iwelumo on 64 minutes on the back of an excellent passage of play, standing the ball up to the back post for the big man to head home his first for the club.
Devonshire turned to his bench to halt the momentum but Chester went three up on 67 minutes when Iwelumo knocked the ball down and play shifted right for Mahon to tee up McConville, who steered past Hamann for his second.
Having turned things around, the Blues now began to focus on defensive duties with the Iron throwing men forward.
Braintree pushed hard but the back four looked far more assured and the frustration grew for the home side with Brown marshaling the rearguard well as the Blues secured all three points.
Chester FC: Hall, Disney (Heneghan 45), Brown, Charnock, Roberts, Mahon, Rooney, James, Winn (Menagh 90), McConville, Iwelumo (Hobson 85).
Subs: Worsnop, Riley.
Goal: McConville 48 and 67, Iwelumo 64.
Booked: Disney, Brown.
Braintree Town: Hamann, Peters, Brundle, Massey, Habergham, Mulley, Davis, Marks, Sparkes, Walker (Bakare 58), Marks (Cox 65).
Subs: Case, Clerima, Pentney.
Goal: Davis (pen) 23.
Booked: Marks, Cox.
Referee: John Brooks (Melton Mowbray).
Attendance: 819.
