Obama is expected next week to announce McDonough, arguably his closest foreign policy aide, as his choice to succeed White House Chief of Staff Jacob Lew, his nominee for treasury secretary.
Former Sen. Tom Daschle, D-S.D., told the Times McDonough will face "a new set of challenges."
"He has an extraordinarily close relationship with the president. What the president wants is a fairly tightly knit, cohesive team that he trusts, rather than to bring in people who would have to learn anew his style and positions," Daschle said.
McDonough, 43, worked for Daschle before joining Obama's team when he was a U.S. senator from Illinois.
White House sources told the Times McDonough is known for taking on problems no one else wants, such as coordinating the response to the terrorist attack on the U.S. Consulate in Benghazi, Libya, that killed Ambassador Christopher Stevens and three other Americans.
McDonough has been described as fiercely loyal to Obama.
"People throughout the foreign policy apparatus found out very quickly that when the national security adviser called, he might be calling for himself or for the president. But if Denis McDonough called, he was really calling for the president," James Mann, author of "The Obamians," a book about Obama's foreign policy team, told the newspaper.