SANTA CLARA, Calif. -- After just one season as the San Francisco 49ers' defensive coordinator, Steve Wilks is out.

"This morning I relieved Steve Wilks of his duties," Niners coach Kyle Shanahan said in a conference call Wednesday that was scheduled just 10 minutes before it happened. "[We're] going to end up making a change here at defensive coordinator. A really tough decision, because [it] really says nothing about Steve as a man or as a football coach. I mean, he's exactly what we wanted as a man. He is a great football coach.

"But just where we're going and where we're at with our team from a scheme standpoint and things like that, looking through it all throughout the year to these last few days, I felt pretty strongly that this was a decision that was best for the organization."

Shanahan on Tuesday mostly dodged questions about whether Wilks would remain as defensive coordinator for a second season. He said he needed more time to sort through his feelings on his staff, though he did say he expected most of his staff to be back.

By Wednesday morning, Shanahan said he realized that "going a different direction" was "something that I have to do."

In Wilks' lone season with the Niners, the defense had its share of ups and downs. A unit that led the NFL in multiple categories in 2022 under DeMeco Ryans -- including fewest points per game allowed (16.3) and defensive expected points added (89.58) -- took a step back in 2023.

San Francisco still finished third in points allowed (17.5) this season, but the 49ers were ninth in defensive EPA (41.48) and sprung significant leaks against the run in the playoffs, allowing the Green Bay Packers, Detroit Lions and Kansas City Chiefs to average 5.1 yards per carry and 149.3 yards per game in the postseason.

Shanahan took ownership of some of those struggles, saying he wanted Wilks to run the same system that had previously been in place with Ryans and Robert Saleh before him.

"I knew that was a challenge," Shanahan said. "It was real tough losing DeMeco. It was tough losing Saleh the year before. We had committed to not just the system, but the players that had been in the system, from our D-line or linebackers. They had played in it for such a long time.

"It was my goal to not have to change all of them, and bringing in Steve, who was unbelievable how loyal he was and him trying to do it, but it just ended up not being the right fit. And it hurt for me to do this, but that's exactly why I had to."

After the defense looked like it wouldn't miss a beat during a 5-0 start, Wilks hit his share of bumps thereafter. Shanahan publicly criticized him for an all-out blitz call before the half that resulted in a Minnesota Vikings touchdown in a Week 7 loss. During the Week 9 bye, Shanahan asked Wilks to move from the booth to the field on game days.

And Shanahan used a timeout on defense with the Chiefs facing a second-and-6 at San Francisco's 37 with 2:48 left in overtime in Sunday's Super Bowl loss, later saying he didn't like the look of the play.

After the Chiefs' win, defensive end Nick Bosa said the Niners weren't prepared for some of the designed running plays for quarterback Patrick Mahomes. During locker cleanout Tuesday, Bosa offered an assessment of Wilks' performance in 2023.

"I think he does a great job with the back end, and obviously we had some issues this year throughout the year," Bosa said. "But that's part of playing a full season, and I think we were playing our best ball at the end."

Linebacker Fred Warner offered a more positive outlook on how things went, noting the Niners finished fifth in takeaways (28) and recorded 22 interceptions, which tied for first in the league.

"I thought it went well," Warner said Tuesday. "I think people are obviously going to be critical just because of, when you go from having the No. 1 defense one year and then a guy comes in and you're not the No. 1 defense again, it's like, 'Oh, well, what happened?'

"Well, I mean there's a lot more that goes into it. And it was a hard job for him all along because he was coming into a system where it was something that he didn't run. He had to come and learn what we did and we were the No. 1 defense a year ago, and it's hard to sustain that type of play. But we still were a top defense in this league, and I think we played our best ball when it was needed."

The 49ers will now begin the search for their third defensive coordinator in as many seasons. Shanahan said he will consider both internal and external options. The benefit of looking internally is that he could find someone who already knows the scheme and would be more of a natural fit, like Saleh and Ryans were.

One thing Shanahan would prefer, however, is a coordinator who is better equipped to tie the defensive front and secondary together. Unlike Ryans and Saleh, both of whom had experience coaching linebackers, Wilks had an extensive background working with the secondary.

"You want to tie things together and Steve was always working to do that," Shanahan said. "There's no doubt about that. But it was just for his background and how it ended up with us, it was harder than it needed to be and I felt it would improve us going a different direction."

Wilks came to the Niners after finishing 2022 as the interim coach of the Carolina Panthers. He had previously coached the Arizona Cardinals in 2018 but was fired after going 3-13. That resulted in Wilks joining a lawsuit initiated by Brian Flores in 2022 against the NFL for racial discrimination in which Wilks alleges the Cardinals did not give him a "fair" opportunity because he is Black and used him as a "bridge" coach.