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Ebbsfleet crashed to their fourth straight home league defeat on New Year's Day.
Michael Cheek and Jaanai Gordon scored at the PHB Stadium as Chelmsford exacted revenge for their 5-1 home thrashing at the Fleet's hands on Boxing Day.
Jamie Day's side have now slumped to eighth in Vanarama Conference South.
The main team news ahead of the game was that manager Day made his playing debut in midfield for Ebbsfleet. Four days after describing their 5-1 home defeat to Basingstoke as "embarrassing", Day's inclusion was one of three changes, with Dean Pooley selected at right-back (Chris Sessegnon having been loaned to Sutton) and Alex Osborn starting a league game for the first time since September.
Billy Bricknell and Sean Shields dropped to the bench, while among the players left out altogether were Matt Godden, Shane Huke, Brendan Kiernan and Michael Corcoran.
Former Fleet defender Yado Mambo started for Chelmsford, who arrived on the back of a 5-3 win at Staines.
Ebbsfleet made a positive start and Anthony Cook dragged a shot wide when a free-kick dropped to him in the box. Anthony Acheampong then met Daryl McMahon's inswinging cross with a glancing header which had to be clawed out by goalkeeper Bradley Watkins to stop it creeping inside the far post.
The visitors posed an occasional threat on the counter-attack and Robert Girdlestone crossed low from the right for Cheek, who was denied by a timely Acheampong intervention in the six-yard box.
But the best chances were being fashioned at the other end.
Watkins caught a beautifully-struck McMahon half-volley and then dived to his right to push out a rocket from Matt Johnson. McMahon then turned inside onto his right foot and curled a shot across Watkins which dropped just the wrong side of the far post.
The efforts kept coming. Johnson shot wide from a similar position and when Joe Howe picked out McMahon on the edge of the box, Mambo blocked his goalbound shot.
Tyrone Marsh had one shot blocked and another saved by Watkins as the Fleet pressed late in the first half - but it was Chelmsford who opened the scoring in stoppage-time.
Leon Redwood's free-kick from the right-hand side wasn't dealt with and Cheek stole in to bundle the ball over the line as the men in red shirts stood and watched.
The nerves returned to Ebbsfleet's play at the start of the second half.
It took them until the hour mark to fashion a chance of any note, Osborn drilling a left-footed shot towards the bottom corner and Watkins pushing the ball behind.
That was to be Osborn's last contribution as he was replaced by Dagenham loanee Shields moments later. Shields and Marsh combined to set up Johnson for strike from 20 yards but his low effort scudded wide.
Kenny Clark almost put through his own goal, against his former club, and was grateful to goalkeeper Brandon Hall for diving acrobatically to keep out his ill-judged header.
It needed another crucial save from Hall to stop Gordon making it 2-0 moments later.
But the home side were finally sunk by a second City goal, 11 minutes from time, when Jaanai Gordon punished some pretty weak defending by nodding in Rohdell Gordon's deep cross at the back post.
Cook swirled a late free-kick wide - but this was another feeble Ebbsfleet surrender.
Ebbsfleet: Hall, Pooley, Acheampong, Clark, Howe, M Johnson, Day (Bricknell 80mins), McMahon, Osborn (Shields 67mins), Cook, Marsh. Subs not used: Turner, Miller-Neave, C Johnson.
Chelmsford: Watkins, Girdlestone, Toner, Hughes, Hickford, Mambo, Sawyer, Redwood, Jaanai Gordon, Cheek (Smith 74mins), R Gordon (Nicolau 84mins). Subs not used: Ekpiteta, Jake Gordon, Freund.
Attendance: 1,069.