The singer, who was voted back into the show earlier this month, has been given the prominent role at the end of the commercial, which was previously taken by Misha B.
Media outlets have claimed that X Factor producers are facilitating a Lily victory by giving her extra attention, but Marks & Spencer insisted it always planned to edit the advert throughout the show's run.
"We said from the start that we would be changing the ad all the way through the series and we have changed it as contestants have left," a Marks & Spencer spokesperson told the Manchester Evening News.
"One slot in the ad does not necessarily take prominence over another one."
Asked whether the company altered the commercial because they no longer view Misha B as the favourite, the spokesman added: "That is absolutely not the case. We have said right from the start that we would edit and change the ad."
X Factor bosses were previously forced to deny claims they had fixed The X Factor for Lily to return after the results of the vote were published online before the phone lines had closed.
Watch the new Marks & Spencer advert below: