Magnolia Bakery may have waited too long to accuse an ex-employee of selling copycat cupcakes — because his business has already crumbled.

The popular chain sued Buba Trawally yesterday for allegedly swiping its closely guarded recipes so he could open the rival Apple Cafe blocks from Magnolia’s flagship in Greenwich Village.

But when The Post visited the Apple Cafe last night, it had a “For Rent” sign in the window.