However, after much discussion with experts, it doesn't sound like surgery will be necessary. Lynch shared what Garoppolo, the team, and foot surgeon Robert B. Anderson concluded.
"I think the most encouraging thing was that his recommendation, which was in line with our orthopedist, was that he didn't need surgery right now ... Right now, we're going to leave it alone, we're going to give it some time to kind of settle down, and then start to ramp him back up.
"At that point, if it's not good, then you might have to go do it. But for right now, the good news is no surgery necessary, and I know Jimmy was excited about that, as were we."
Garoppolo has missed 16 games over the past three seasons and might not be available until Week 15 at the earliest. There has been a lot of speculation surrounding his NFL future and status with the 49ers beyond this season.
Lynch confirmed a report that VP of player personnel Adam Peters traveled to Boise, Idaho last week to watch BYU quarterback Zach Wilson, but added that the team scouts many quarterbacks each year.
"Here's what I know about Jimmy Garoppolo, and I think I've been consistent," Lynch said. "We're a better football team when he's out there. We win a lot of games when he's out there. We struggle to win without him.
"So, people can try to pick his game apart, and I do believe a lot of this year, Jimmy probably hasn't played up to his standard. I think a lot of that, he's been somewhat compromised with his health since he had that high-ankle in the New York Jets game.
"Think about prior to the ankle injury in that game. I believe he was 12-of-14. He was our player of the game. We have a lot of belief in Jimmy."
Garoppolo has completed 67.1 percent of his passes for 1,096 yards with seven touchdowns and five interceptions in six games this season.
You can listen to the entire conversation with Lynch below.
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