The England international wanted leave United at the end of last season and handed in a transfer request, according to former boss Sir Alex Ferguson.
Rooney reportedly told Moyes that he was unhappy with how he was treated last season and denied asking to leave the club.
A source told The Sun: "There is little doubt the new boss wants to keep Wayne. Any suggestions the two don't get on is complete rubbish.
"It was an amicable meeting but it gave Wayne the chance to get a lot of things off his chest.
"He's always denied handing in a transfer request and like all top players, he was upset to be dropped, especially for the Real Madrid match."