Moya will also coach at Nadal's recently established tennis academy in Mallorca.
2016 followed a familiar recent pattern, with a wrist injury ending his hopes of a 10th French Open crown on his favorite clay, but he returned to win Olympic gold in the Rio in the doubles with Marc Lopez.
The Spaniard will begin his new season at a six-man exhibition event in Abu Dhabi from December 29 to 31 as he builds up to the Australian Open in January.
"I am sure that together with Toni, Francis and the rest of the team we have a great common project," said Moya.
"Rafa is a special player and above all a great person and friend on which I have a lot of trust and confidence that will be able to continue winning important titles."
Moya recently severed ties with Milos Raonic, after helping the Canadian to a career-high three in the world rankings by the end of the season.