City were defeated at AFC Wimbledon, having had to play most of the match with 10 men.
Head coach Michael Skubala stuck with the side which got the season off to a winning start against Reading, including the same bench. AFC Wimbledon included former Imps midfielder Ali Smith in their starting line-up.
The opening period was cagey, with Rob Street getting a good cross in from the right.
George Wickens had to be alert as the home side earned a succession of corners - with two deliveries from Myles Hippolyte placed right on the crossbar necessitating the keeper tipping the ball over. The third delivery was claimed by Wickens.
Chances came as the game opened up, with Tendayi Darikwa flicking a ball through for Tom Bayliss’ run - on this occasion the cross was cut out for a corner.
Jack Moylan fired over after 21 minutes, having cut inside after collecting the ball from Conor McGrandles.
The dynamics of the game changed after 23 minutes. with Adam Jackson shown a straight red following a challenge on Matt Stevens.
City had to be patient as the home side probed, but did a great job of limiting chances until a break down the right saw Sonny Bradley penalised for handball in the area after 42 minutes.
Stevens stepped up to take the set-piece, putting the Dons ahead with a smart finish into the bottom right corner.
It would have been easy for Bradley to have been affected by conceding the penalty, but he was in the thick of things with a block to deny Stevens his second of the game.
City were having to be patient even though they now trailed in the match, and there were calls for a penalty when Jack Moylan went down in the area having looked to have had contact with Hippolyte.
There was one change for the Imps at the interval, with Tom Hamer sent on. Street was the man who had to make way.
Hamer slotted in alongside Bradley at centre-back, and brought an added threat with his long-throw.
City again had to be patient, but found themselves having more and more of the ball.
The best chance to draw level came after 56 minutes when Darikwa found himself leading an attack and running at a defender. He tried to play in Moylan, with an incredible run and sliding interception from Wimbledon’s Joe Lewis denying the Irishman a shot on goal.
Moylan cut a frustrated figure moments later when he again found himself on the floor in the area, this time after tangling with Ryan Johnson, only for referee Matthew Russell to again dismiss the appeal.
Both head coaches made changes to personnel as the game entered the final 30 minutes, with Freddie Draper and Ethan Hamilton sent on for the Imps.
Another Hamer long-throw provided an opportunity after 68 minutes. The ball found its way through to Hamilton but the ball bounced up quickly at him and his reaction header went just over the bar.
City continued to probe and looked threatening from set-pieces, but hopes of a comeback were effectively extinguished when Nathan Asiimwe fired home from a corner-kick.
There was one final throw of the dice from Skubala as young forward Zane Okoro was sent on for fresh legs, but it was not enough to rescue anything from the game.
AFC Wimbledon: Bishop, Asiimwe, Seddon (Sasu, 75), Reeves, Johnson, Browne (Maycock, 75), Smith, Stevens (Hackford, 60), Hippolyte (Orsi, 59), Lewis (Harbottle, 90+2), Ogundere. Subs not used: McDonnell, Kelly.
Imps: Wickens, Darikwa, Jackson, Towler, Hackett (Okoro, 79), Bayliss, Collins (Draper, 63), Moylan (Hamilton, 63), McGrandles (Ring, 70), Bradley, Street (Hamer, 45). Subs: Jeacock, Okewoye.
Referee: Matthew Russell.
Attendance: 8,067 (789 away).
