Jamie Cureton opened the scoring in the 55th minute, but Blues responded well and levelled 11 minutes later when substitute McClure fired low past Scott Brown.
However, the killer blow was struck just 60 seconds later when Deering’s cross took a deflection off a defender and looped over a despairing Matt Ingram.
Paris Cowan-Hall shrugged off a calf injury to replace Steven Craig, who dropped to the bench, while Anthony Stewart and Leon Johnson formed the centre-back partnership with Kortney Hause missing out through injury.
Billy Knott and Dean Morgan also started as Gareth Ainsworth made five changes to the side that pushed League 1 side Swindon Town all the way in the Johnstone's Paint Trophy on Tuesday.
The majority of the opening 10 minutes was played in midfield, but Billy Knott did try his luck from the edge of the area, only for his strike to fly over.
Jamie Cureton had the first effort on target and it came in the 11th minute, but Matt Ingram was equal to his powerful strike and parried away at the near post.
Byron Harrison squandered a golden chance to give the visitors the lead in the 16th minute when he received the ball inside the area from Deering, but scuffed harmlessly wide whilst well placed.
It took the Wanderers 19 minutes to get fully into their stride, but when they did they produced a move that the visitors struggled to cope with.
The ball was fizzed into Knott’s path and his instinctive backheel freed Lewis who crossed low into the area. Kretzschmar steadied himself before seeing a shot blocked and the ball fell to Morgan whose low strike was well kept out by Scott Brown’s legs.
Deering blazed over the bar, before Scowen saw a shot blocked on the edge of the area, but aside from Chairboys’ earlier moment of magic, neither side were creating any chances of note.
Ingram had to be alert to tip over Jason Taylor’s deflected shot 10 minute before the break and Blues’ No.1 then did well to react quickest to Deering’s through ball and smother the ball ahead of the advancing Byron Harrison.
The final chance of the half fell to Anthony Stewart, but he fired wide from 20 yards after Cheltenham failed to deal with a set-piece.
Cheltenham were fast out of the traps in the second half and Richards saw a 20-yard free-kick deflect wide off the wall.
Ainsworth made his first change in the 54th minute with Matt McClure replacing Morgan, but the visitors struck 60 seconds later. Deering’s cross was cleared as far to Taylor and his mis-hit shot fell to Cureton who fired low past Ingram into the far corner.
It was almost two three minutes later when Richards picked out Cureton, but the striker half-volleyed wide.
Brown came to the visitors’ rescue on the hour when he kept out McClure’s close-range header after the substitute had been superbly picked out by Lewis’ cross.
Lewis had the next chance himself, curling over the bar from the edge of the area after Wood’s low cross was only half dealt with.
Wanderers had responded well to going behind and levelled in the 65th minute when Knott found McClure in the area and he clinically fired low across Brown and into the far corner.
However, parity only lasted 60 seconds as Deering’s intended cross took a huge deflection off a Wanderers defender and looped over Ingram.
Blues’ keeper produced a stunning save to keep his side in the contest as he clawed Elliott’s header from a Richards free-kick away for a corner.
Matt Bloomfield was introduced in the 73rd minute and Ainsworth made his final change eight minutes later with Craig replacing Cowan-Hall.
Wanderers pushed forward in search of a late equaliser and McCoy picked Craig out in the area, but his flick ricocheted off a defender and forced Brown into a fine reflex stop.
That was to be the closest they came though, as Cheltenham held out for the win.
Wanderers: Ingram, McCoy, Wood, Stewart, Johnson, Cowan-Hall (Craig 81), Lewis (c), Scowen, Kretzschmar (Bloomfield 73), Knott, Morgan (McClure 54).
Subs: Horlock, Doherty, Spring, Morias.
Cheltenham: S Brown, Jombati, Braham-Barrett, T Brown, Elliott (c), Noble (Lowe 90), Deering (Gornell 84), Taylor, Richards, Cureton (Penn 75), Harrison.
Subs: Roberts, Hanks, Vincent, Kotwica.
Attendance: 3,207 (189)