John Lynch went to the podium during the NFL draft combine on Tuesday in Indianapolis and sent a strong message to the 49ers’ Brandon Aiyuk: We want you to stay put. That is most probably obvious, but what is less clear is whether Lynch and the 49ers can make that actually happen given the restraints on their salary structure.

Also less clear: Whether Aiyuk wants to stay in San Francisco at all.

But let’s start with what Lynch had to say at the combine, where he acknowledged the 49ers’ “challenges” but also highlighted the team’s record on getting players signed.

“We have some challenges,” Lynch said, per Pro Football Talk. “We have a lot of good players, a lot of good players who we’ve rewarded. Brandon’s one that we think incredibly highly of, one of my favorite guys around our building, the way he approaches the game. He’s a competitor. He’s a warrior. He plays with such physicality, also with grace, in the way some of the positions his body can get into.

“And then he’s got a flair for making plays when [they] matter most, and he’s served us very well as a franchise. And I think we’ve got a nice track record of extending the players that are important to us, and Brandon’s the guy we want to keep around for a long time.”

49ers’ Brandon Aiyuk Had a Breakout Year

There’s plenty of reason or Lynch to want Aiyuk in San Francisco. Aiyuk racked up 1,342 yards on just 75 catches last year, and his 17.9 yards per catch were No. 2 in the NFL. He formed what seemed to be a strong chemistry with quarterback Brock Purdy throughout the season, especially with the team’s other top receiver, Deebo Samuel, hurt for two games and parts of others.

But Aiyuk won’t be cheap. Even with the $30 million spike in the salary cap, it will difficult for San Francisco to carve out enough room to keep Aiyuk, who turns 26 next month and is already a Top 5-10 receiver in the NFL.

Technically, Aiyuk is under contract on his fifth-year option next season, at $14 million. The 49ers could attempt to bring him back next season at that number, but there is just about a 100% chance he would hold out for a new deal. Spotrac projects Aiyuk for a contract at $23 million per year, and expects him to warrant an extension of four years and $92 million.

The 49ers could structure things so that they squeeze Aiyuk in this year—with a chance to return to the Super Bowl—but they would certainly have to make changes next season as their payroll explodes.

Seeking an Escape From San Francisco?

There’s also the issue of whether Aiyuk wants to be back, a puzzling one, no doubt. Aiyuk was the leading receiver on a team that includes stars Deebo Samuel and George Kittle, plus versatile running back Christian McCaffrey. There are only so many plays in a game, but it appeared Aiyuk was unhappy with how much he was being used.

Aiyuk’s close friend Draysean Hudson pointed out earlier this month that Aiyuk had only three catches in the Super Bowl and added, “This is the exact reason why we leaving San Francisco.”

Brandon Aiyuk’s Brother (Best Friend) On IG pic.twitter.com/WedP0QYiZ8

— WayneBreezie (@thewaynebreezie) February 13, 2024

That sounded a bit harsh, of course. It was, though, the third straight playoff game that he had only three catches.

When those posts were brought up to Aiyuk he did not attempt to brush them off, saying he would stay with the 49ers only if it were, “the right move.” He also seemed bothered on social media by his lack of postseason catches when he posted, “Don’t forget what got you there.”

It’s a tough situation for the 49ers, one made only more difficult by Aiyuk’s post-Super Bowl social media activity. But Lynch, for one, still is hoping he will be back.