"I don't expect these issues to impact his ability to prepare for the upcoming season," said team physician Tom Clanton, who operated on McGrady's knee.
Loose tissue was cleared out of the left knee and left shoulder. McGrady sprained his shoulder against Sacramento on March 24 and wore padding to protect it for the rest of the season, which ended last Friday against Utah in the first round of the playoffs.
McGrady revealed midway through the series he was having a recurrence of the same knee problems that kept him out of 12 games in December and January. He took painkilling injections during the Utah series.
"It's really going to help him recover and be pain free in those areas going forward," general manager Daryl Morey said Wednesday. "Those are two areas that have been nagging Tracy for a while -- not as acute as we saw this season -- but they've been nagging him."
The procedures, both considered minor, were done Tuesday.
McGrady averaged 21.6 points, 5.1 rebounds and 5.9 assists this season. He averaged 27 points, eight rebounds and seven assists in the playoffs, but the Rockets lost to the Jazz in six games. McGrady is 0-for-7 in the playoffs in his 11 seasons.
Point guard Rafer Alston and forward Shane Battier also will have surgery soon, Morey said. Alston injured ligaments in his right ankle in Game 6 in Utah and Battier hurt his left ankle late in the regular season.
Morey met with Dikembe Mutombo on Tuesday and said the 41-year-old backup center will decide in a week to two weeks whether he will return for an 18th season or retire. The 7-foot-2 Mutombo capably filled in when Yao Ming broke his foot in February, averaging 16 minutes and three points a game.
"If he decides to come back, it's a good thing for us," Morey said. "It creates another option or a possibility for us going forward."