More on KentOnline
Former Gills striker Cody McDonald had a penalty saved in Ebbsfleet's final pre-season friendly on Saturday.
McDonald, back in Kent with his new club AFC Wimbledon, was kept off the scoresheet by Fleet keeper Nathan Ashmore.
But it was the League 1 visitors who prevailed in another good test for Ebbsfleet ahead of Saturday's National League opener at Guiseley.
Ebbsfleet were unchanged from last Saturday's 1-1 draw with Southend, with injuries again ruling out centre-half Kenny Clark and midfielder Dean Rance.
Deji Oshilaja, who like McDonald left Gillingham this summer, started for Wimbledon.
The visitors bossed the first half in grey, drizzly conditions at Stonebridge Road.
Egli Kaja outmuscled Jack Payne just outside the Fleet penalty area and dragged a low shot wide before the home side allowed a Callum Kennedy cross to bounce in the six-yard box.
It took a superb block from Dave Winfield to deny Andy Barcham the opener on 18 minutes after the former Gills man had collected Kaja's low cross from the right.
When the home side did get forward, left-back Jack Connors saw his cross-shot deflect away from danger.
A neat turn from Myles Weston drew a foul 20 yards from the Wimbledon goal although Jack Powell's free-kick struck the wall. Powell then delivered a deep corner which reached Winfield at the far post but his header was easily gathered by goalkeeper George Long.
The visitors missed a great chance to take the lead two minutes before half-time. Kennedy's cross from the left picked out another former Gills player, Barry Fuller, but the right-back failed to hit the target with his free header.
Fleet made a double substitution at half-time, Danny Kedwell and Andy Drury the men to come on, and a minute later, an injury to Jack Connors saw Bagasan Graham enter the fray.
Luke Coulson moved to right-back as Daryl McMahon took the opportunity to look at his newest recruit in a different position.
But Coulson was caught out by McDonald 10 minutes into the second half, giving away a penalty for handball. McDonald took the spot-kick but Nathan Ashmore, diving high to his left, denied him with a strong save.
Kennedy saw a free-kick skim the top of the wall and Wimbledon were ahead from the resulting corner. Francomb delivered it and Fuller swept a volley low past Ashmore.
The lead only lasted three minutes though. Fleet thought they had a penalty of their own when Kedwell's excellent ball into Weston's feet saw the midfielder fouled right on the 18-yard line.
Long got a hand to Powell's free-kick but couldn't keep it out of the top corner.
Ebbsfleet were now enjoying their best spell of the game and Drury fired a low strike wide before McQueen latched onto Powell's pass, took a touch and forced Long to tip his shot over the bar.
The visitors retook the lead on 68 minutes, Barcham rifling a fine effort into the top corner.
Dons substitute Osaze Urhoghide missed two glorious chances to make it 3-1, wastefully failing to hit the target on both occasions.
Powell almost added to his free-kick collection from at least 25 yards out, bending the ball towards the top left-hand corner only for Long to claw the ball out at full stretch.
Kedwell and Yado Mambo had clear penalty shouts waved away by referee Alan Dale in the closing stages and the last kick of the match saw another Powell free-kick held by Long.
Ebbsfleet: Ashmore, McCoy (Drury 46mins), Winfield, Magri, Connors (Graham 47mins), Powell, Payne, Coulson, Weston (Mambo 71mins), Mills (Kedwell 46mins), McQueen (McLean 76mins). Subs not used: Miles, Cook, Shields.
AFC Wimbledon: Long, Fuller, Kennedy, Oshilaja (Urhoghide 69mins), Kalambayi, Francomb, Abdou, McDonald, Egan, Barcham, Kaja. Subs not used: Tranev, Ashley, Evans.
Attendance: 671.