Substitute James Horsfield, a regular at U18 level, grabbed the Blues’ goal on a frustrating night for Attilio Lombardo’s men.
This was City’s first Manchester Senior Cup involvement since beating Stockport County on penalties back in November, but Lombardo’s young Blues last visited Leyland just 10 days ago for a league encounter with the Trotters.
On that occasion, a side including Micah Richards and Maicon was unlucky to be held to a 1-1 draw.
This match was the first of three games in three days at U21 and U18 level, meaning it was a much-changed side which took to the field in Leyland.
Jose Angel Pozo was ruled out with injury, but there were starting berths for Felipe Mancini, and U18s centre-back Tosin Adarabioyo. Horsfield joined the fray as a substitute after an hour.
The match began slowly with few real chances for either team in the opening stages. City’s stand out player, Seko Fofana, found Sinan Bytyqi with a perfect ball to the right wing, but the youngster shot high and wide after wriggling through the Bolton defence.
Fofana himself forced a good save from the Bolton keeper from a free kick, while Robert Hall smacked a long range shot just wide for the home side.
It was the Trotters who took the lead in a scrappy match when ex-City man Matt Mills headed in from a corner after 37 minutes.
They extended their lead after half time, Chris Lester firing in from a tight angle and Jack Sampson putting the ball in the net after a defensive mix-up.
City kept fighting but couldn’t create many chances.
Horsfield made some good runs and crosses down the right and was rewarded with a goal after 75 minutes. Fofana picked out another fantastic pass to the right wing and Horsfield’s shot bounced in off a defender.
While Fofana pulled the strings in City’s midfield, Angus Gunn made several impressive stops late on, including a great block when one on one with the striker, and pouncing on a low header from a corner just before the final whistle.
Next up, the EDS have a Lancashire Senior Cup tie on Friday against Wigan to tackle and the short turn-around is sure to lead to fresh faces in the line up.
We’ll bring you goal updates from that game on twitter and a match report after full time on mcfc.co.uk.