Jeffers, who was making his full debut after coming on as a substitute against Truro, opened the scoring in spectacular fashion with a superb scissor kick after just 10 minutes.
The Clarets were forced into replacing their captain, Billy Bricknell, with less than half an hour played. His replacement though, Shamir Mullings, wasted little time in doubling City’s lead with a volley from close range.
City would go on to miss a plethora of chances as their visitors posed little threat to the Chelmsford back line as the Clarets secured their first win of the season.
After enduring the long trip to Truro on Saturday Stringer promised to freshen things up ahead of the visit of Margate and the Clarets boss made two changes to his side from the weekend, replacing Jake Reid and Luke Daley with Shaun Jeffers and Bagasan Graham.
And it wasn’t long until Jeffers was making his presence felt, stinging the palms of Lewis Ward in the Margate goal within three minutes.
There was nothing though that Ward could do about Jeffers’ and Chelmsford’s opening goal of the evening after Anthony Church headed the ball into the area, teeing up the former Yeovil striker to acrobatically send the ball into the bottom corner with a scissor kick.
It was the perfect introduction to the Claret fans for Jeffers who was a constant threat to the Gate back line which included former City defender Yado Mambo.
Chelmsford were dealt a blow just before the half hour mark when Billy Bricknell, who had been struggling after an accidental clash with Chris Bush, was forced to depart.
The City skipper was replaced by Shamir Mullings whose late header rescued a point for the Clarets at the weekend. And the six-foot-plus striker wasted little time in grabbing his opportunity from the bench by scoring Chelmsford’s second.
After working the ball out to the right, Robbie Willmott cut inside on to his left foot before arching in a perfectly measured cross towards the far post that deceived the Margate defender, leaving Mullings to smash home the volley from close range to make it 2-0.
Just before City’s second Margate did carve out a good opening through former Claret Michael Thalassitis, and with last season’s top goal-scorer Elliot Buchanan up front with him Chelmsford had to be on their metal defensively.
City though will feel they should have had an opportunity for a third goal before the break from the penalty spot when Mambo appeared to up-end Mullings in the area but the referee Josh Smith waved off Chelmsford’s claims to the bemusement of Rod Stringer.
Chelmsford continued to press for a third in the second half with Max Cornhill going close with a header early on, and Jeffers had a glorious chance to extend City’s lead when he was let through on goal only to be denied by the left hand of Ward.
Margate were restricted mostly to attempts from distance with Alex Osborn and substitute Lewis Taylor trying from range, but City’s defence stood firm with Joe Welch confidently coming for almost everything in the air.
With the game all but sewed up Margate had their clearest chance of the evening fall to Thalassitis in injury time when Ali Fuseini's shot was only parried by Welch, Thalassitis and Buchanan got in each other's way going for the rebound preventing the former Clarets-loanee from bundling the ball beyond Welch.
Chelmsford would hold on comfortably to earn themselves their first win of the new season ahead of the visit of Dartford on Saturday.
1. Joe Welch
2. Ashley Miller
3. Daniel Blanchett
4. Max Cornhill
5. Mark Haines
6. Chris Bush
7. Robbie Willmott
8. Anthony Church
9. Shaun Jeffers
10. Billy Bricknell (c)
11. Bagasan Graham
12. Luke Daley (On for Robbie Willmott 78’)
14. Adam Bailey-Dennis
15. Shamir Mullings (On for Billy Bricknell 29’)
16. Hugo Skepelhorn (On for Bagasan Graham 75’)
19. Frankie Merrifield
1. Lewis Ward
2. Adam Cash
3. Aaron Tumwa
4. Matt Johnson
5. Yado Mambo
6. Manny Parry
7. Scott Donnelly
8. Luke Moore (C)
9. Michael Thalassitis
10. Elliot Buchanan
11. Alex Osborn
12. Brett Johnson
14. Lewis Taylor (On for Matt Johnson 54’)
15. Ali Fuseini (On for Scott Donnelly 54’)
16. Daniel Akindayini
17. Marcel Barrington (On for Luke Moore 70’)
Chelmsford City: Shaun Jeffers 10’, Shamir Mullings 38’
Chelmsford City: Shamir Mullings (Dissent - 45+1’)
Margate: Luke Moore (Foul – 45+2’)
Referee: Josh Smith
Assistant Referees: Lee Grimsey & Darren Knox
City Man of the Match: Shaun Jeffers
Match Sponsor: Big Cars