Liam McAlinden’s first goal of the season after 20 minutes gave them three points and saw Derek Adams’ players complete the double over a visiting side who had started the day top of the table.
Adams made two changes to the team which won at Harrogate Town seven days earlier.
Sam Lavelle returned from suspension, replacing the similarly banned Nat Knight-Percival in the centre of defence.
McAlinden was handed a start in the absence of Alex Kenyon, missing after rolling his ankle in training on Friday.
The changes also brought a different shape with the Shrimps deploying a midfield diamond and McAlinden joining Cole Stockton up front.
Both sides began brightly with Lavelle heading over Aaron Wildig’s corner and Morecambe keeper Kyle Letheren holding Sam Smith’s early effort.
The Shrimps looked to get joy in behind the visitors’ back three with narrow offside decisions going against McAlinden and Carlos Mendes Gomes.
At the other end, Ben Tozer’s long throws were a nuisance with one seeing two Alfie May shots blocked.
Liam Sercombe also volleyed off target before the Shrimps took the lead with McAlinden bursting through and finishing clinically.
John O’Sullivan fired over before seeing an effort ruled out for offside as Adams’ players sought a second goal.
However, it was the visitors who had the better of the play up until the break, albeit without forcing Letheren into a save.
Lewis Freestone headed over from a corner with Sercombe off target and seeing a shot blocked as the Shrimps retained their lead at half-time.
Having kept his first clean sheet for the Shrimps at Harrogate, Letheren preserved Morecambe’s lead early in the second half with a fine reaction save to deny May.
Another stop followed with the hour mark approaching, this time from Callum Wright, as Cheltenham began to dominate possession.
Wright came close again moments later, turning Finn Azaz’s cross narrowly over seconds after a Morecambe counter-attack had broken down.
Letheren held efforts from Sercombe and Smith before the Shrimps were forced into a change with Harry Davis limping off, replaced by Stephen Hendrie.
That meant a reshuffle with Liam Gibson moving into Davis’ position with Hendrie slotting in at left-back.
Lavelle headed over from another corner for the Shrimps, whose attacks became increasingly sporadic with the visitors piling on the pressure.
Letheren spilled a shot from Indiana Vassilev, the home defence coming to the rescue, before Smith shot wide in the first of five added minutes.
That was close as they came as the Morecambe defence held out for another three points.
Morecambe: Letheren, Mellor, Lavelle, Davis (Hendrie 68), Gibson, Diagouraga, Wildig, O’Sullivan (Pringle 90), Mendes Gomes, McAlinden (Cooney 66), Stockton. Subs not used: Halstead, Denny, Price.
Cheltenham Town: Flinders, Long, Tozer, Freestone (Vassilev 83), Blair (Azaz 50), Thomas, Sercombe, Wright (Williams 78), Hussey, May (Chapman 83), Smith. Subs not used: Harris, Horton, Addai.
Referee: Marc Edwards.
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