The firm that manages the advertising space requested for the poster to be edited to hide the statue's nudity.
DRG Group, which owns Glasgow's Barolo restaurant, said it was "surprised" by the response to the advert - which shows the Renaissance sculpture eating a slice of pizza.
It created a new version of the poster that hides the statue's crotch area.
Nadine Carmichael, head of sales and marketing, said: "We had artwork in place and discussed if we could cover the crotch with a flag.
"We got stickers made and the feedback was that they weren't actually big enough.
"Our next port of call was to show Michelangelo from the waist up. We got there in the end."
DRG said it wanted to use classic Italian art to showcase the restaurant on the public transport network, with the Mona Lisa also discussed as a possible candidate.
Michelangelo's 5.17m (17ft) statue is one of the most famous pieces of Renaissance art.
Completed between 1501 and 1504, it depicts a naked David, the Biblical figure who kills the giant Goliath.
Global, which manages the advertising space, has been approached for comment.