Lyon will be examined on Wednesday by noted orthopedist Dr. James Andrews in Florida. The procedure is scheduled for Thursday.
The right-handed closer has tears in his rotator cuff and his labrum, plus a problem with the biceps tendon. He went on the disabled list last week, only a few days after returning from a monthlong DL stint.
"There's obviously a lot of things going on in there," Lyon said. "Hopefully we'll get in there and get it fixed and get it taken care of."
Lyon is hoping Andrews will have a game plan to solve all of the problems in one surgery.
"Everyone has their opinion on it, but really until you get in there you can't really see what's going on," Lyon said. "I think talking to him Wednesday, we'll have a better understanding of what we're going to be going into."
The tendon in the biceps is causing him the most problems. It goes beyond pitching, too. He can reach for something or leave his arm in one place for a long time and it starts to hurt.
"I just want the pain to go away," Lyon said. "Hopefully that's what we can do. Pain is to the point right now where you don't even want to do anything."
Lyon is 3-3 with an 11.48 ERA in 15 games this season. His numbers were inflated by allowing eight earned runs over three outings during his brief try at returning between DL stays.
Last year, he had 20 saves with a 3.12 ERA in 79 appearances.
Bullpen problems are a big reason the Astros have the worst record in the majors. They've blown a league-high 15 save chances, four by Lyon.
Astros manager Brad Mills was hesitant to call this a season-ending injury. Lyon said that's almost a given.
"I might be picking up a ball maybe at the end of the season, but it wouldn't be enough to go out there and pitch," Lyon said. "Obviously the sooner I can pick up a ball and throw the better I'm going to feel for next season. .... I think this is the step in the direction to get healthy."
Lyon, 31, has one year left on his contract.