SANTA CLARA, Calif. — Even as the San Francisco 49ers held out hope that a Monday morning MRI would show that defensive end Nick Bosa had avoided a serious right knee injury, Bosa himself was already resigned to what the imaging would indicate.

Which is why, when Kyle Shanahan spoke to Bosa after the win against the Arizona Cardinals on Sunday night, Bosa told his coach to expect the worst: a torn ACL in his right knee.

As it turned out, Bosa, who has torn ACLs in both knees previously, was correct. The tests revealed he did have a torn right ACL, and he will miss the rest of the season, Shanahan said Monday afternoon.

“He was pretty confident that he did it,” Shanahan said. “You could tell walking on the field, seeing his face and could tell talking to him last night just how sure he was of it and knowing his body, and then an MRI confirmed it this morning.”

Bosa, 27, will need season-ending surgery once the swelling in the knee subsides, and the Niners will move forward without one of their defensive stalwarts and the 2022 NFL Defensive Player of the Year. The 49ers will get almost $7 million in salary cap relief in 2026 because of their insurance policy for a season-ending injury, a source told ESPN’s Kalyn Kahler.

If there’s any silver lining to Bosa’s injury, it’s that the tear to the ACL wasn’t accompanied by damage to any other ligament, Shanahan said.

“I was told it’s as clean as it gets,” Shanahan said. “In terms of if you have an ACL, I was told that’s the kind that you want.”

Theoretically, that should make for an easier recovery for Bosa, who has been through them before. Bosa partially tore the ACL in his right knee as a senior in high school and tore the ACL in his left knee during Week 2 of the 2020 season.

Bosa sustained his most recent injury with about a minute left in Sunday’s game against the Cardinals. He was rushing quarterback Kyler Murray from the left side and engaged with left tackle Kelvin Beachum when guard Evan Brown came over for a double-team and knocked Bosa to the ground.

Bosa’s right knee appeared to bend awkwardly as he went down and Murray’s pass fell incomplete. Bosa then walked slowly to the sideline, where the Niners’ training staff began working on him as he laid on his back.

After a few moments, Bosa walked to the medical tent, where he remained for about five minutes before emerging. He spent the next couple of minutes doing some stretching and high knees but eventually made his way to the locker room.

Shanahan said Bosa didn’t give him a detailed explanation of how he was injured but suggested it was bad luck with how his leg got caught up.

“It’s just how those things happen a lot, especially with ACLs,” Shanahan said. “They happen on air the majority of the time, and I know it was his right leg and he just got it caught right there and it went right away.”

Although initial testing for an ACL tear on the sideline didn’t immediately suggest that Bosa seemed to know what was happening in real time, the television broadcast spotted Bosa giving a thumbs-down to family members in the stands as he ambled to the locker room.

From there, he did not return to the game and was ruled out at halftime. After the game, Shanahan said that the initial test of the ACL on the sideline hadn’t shown a tear but cautioned that Bosa and the team were still concerned about the possibility of a serious knee injury.

Bosa relayed those concerns to Shanahan on Sunday night.

“He had a pretty good idea of what we were going to find out today, but obviously, he is bummed out,” Shanahan said. “Nick can handle anything, and he’s going to handle it like he always does, which will be great. But obviously, he was bummed out from not being able to finish out this year and especially how good of a year he was having so far.”

In the first two weeks before the injury, Bosa had two sacks, eight pressures, 15 tackles and a 21.9% pass rush win rate. He had made game-saving sacks late in wins against the Seattle Seahawks and the New Orleans Saints.

Bosa’s 142 quarterback hits are the most in the NFL dating to the 2021 season. Since Bosa entered the league in 2019, the 49ers are 65-32 in regular and postseason games with him playing and 6-12 when he hasn’t played.

Without Bosa, a Niners defense that already featured eight new Week 1 starters from 2024 to 2025 will be even more dependent on young players and recent additions.

Rookie Mykel Williams, Bryce Huff, Yetur Gross-Matos and Sam Okuayinonu are the remaining defensive ends on the roster, with Robert Beal Jr. and Trevis Gispon on the practice squad.

“You don’t just replace a guy like Nick,” Shanahan said. “Everyone’s got to continue to get better at everything.

“When you lose your better players, it gets harder. But throughout this year, I expect all of our players to get better as it goes. And that’s stressed even that much more when you lose a great one like Nick. Lots of guys obviously will have to step it up as it goes, but I believe that’ll be more by committee than any individual.”

As for potential trade options, Shanahan offered his usual stance that the Niners would always look into their options, but he didn’t sound as if he was in a hurry to make a move.

“We will look at trades like we always do, but there’s got to be trade options that make sense for you and another team,” Shanahan said. “You can’t just do that stuff just to do it.”

Elsewhere on the injury front, Shanahan said quarterback Brock Purdy (toe) will continue to get more involved in practice on Wednesday, and the team will see if he has any limitations before deciding if he’s ready for a bigger practice workload.

Backup quarterback Mac Jones (knee) is considered day-to-day, as are defensive tackle CJ West (thumb), cornerback Renardo Green (neck), wide receiver Jauan Jennings (ankle, shoulder) and defensive end Williams (wrist).

Wideout Demarcus Robinson also can return this week. He was removed from the reserve/suspended list on Monday afternoon.