The 49ers are no longer among the NFL’s unbeaten teams after falling to the Falcons 29–20 on Sunday. San Francisco was bound to lose at some point, but this loss also put the team’s weaknesses on display: the defense and special teams must improve. 

By starting 6–0, the 49ers cemented themselves as one of the league’s best teams, jumping to the top of power rankings and reemerging as a Super Bowl contender. Now, they’ve shown they also have work to do—especially ahead of the trade deadline.

The 49ers’ pass rush disappears again vs. the Falcons

The 49ers’ defense did a good job limiting Bijan Robinson and the Falcons’ run game, holding him to 3.6 yards per carry, but their lack of a pass rush and discipline as a unit proved costly. The 49ers finished last in the NFL in sacks last season, and started 2026 slow again, registering just six sacks through the first four games. The unit showed improvement by recording nine sacks in wins over the Commanders and Seahawks, but struggled to continue getting to the quarterback on Sunday. They did not sack Michael Penix Jr. once, and pressured him only three times during the entire game, per David Lombardi. Penix had been sacked eight times in his previous two games, including five times against the Bears last week. 

San Francisco will be getting Nick Bosa back, but the loss emphasized the need to add to the defensive line at the deadline, especially since Bosa has not played a full season since 2023. The 49ers were already predicted to be in the market for a receiver, but should look to add a player such as Khalil Mack or DeForest Buckner to their line.

Alongside the lack of pass rush, the 49ers have committed too many penalties in their past two games, helping both the Commanders and Falcons sustain key drives that resulted in points. Before the first half ended, Osa Odighizuwa hopped offsides on fourth-and-4, giving the Falcons a free first down so they could gain more yards and kick a field goal. Later the 49ers failed to get off the field on the Falcons’ drive to go up 26–14 because of a defensive holding penalty on 2nd-and-20 and then a pass interference penalty on 3rd-and-8. The 49ers have promise in their hard-hitting young secondary and have largely been good at minimizing big plays, but need to clean up some of these penalties as they head into the second half of the season.

The 49ers have a special teams problem

The Rams have been rightfully criticized heavily for their special team unit, but the 49ers’ issues  in the third phase of the game have been overlooked. Prior to the 2025 season, special teams was often a weakness of the 49ers. They made an effort to improve the unit last season by cutting Jake Moody, signing Eddy Piñiero and trading for kick returner Skyy Moore. The results were good, and the 49ers became a top-ranked team on special teams. Those results, however, haven’t carried over into 2026. 

Piñiero has regressed. He has made just six-of-nine field goal attempts (66.7%), which ranked 32nd heading into Sunday (he did not attempt a field goal against the Falcons). Through Sunday’s game, he has missed four extra points. This includes a missed extra point as the 49ers attempted to come back against the Falcons. Had he made that extra point, the 49ers still would have been within one score of the Falcons when they got the ball back after Atlanta’s final field goal.

Outside of Piñiero, their return game has not been as good since Moore’s departure. They allowed two long returns to the Falcons, and multiple returners have muffed kicks for the 49ers this season. Special teams has only played a part in one loss for the 49ers so far, but certainly could come back to haunt them again if they do not improve the unit.

“All the way through, I’m a believer, on the road you always have to pack your defense. You pack your defense, you pack your special teams,” Fred Warner said after the loss. “I feel like we were ready for the challenge to come out and play our best game and unfortunately we just didn’t do that. I feel like we had so many opportunities to take the ball away.”

The offense played a part in the loss, but isn’t a long-term concern

The 49ers’ offense, of course, isn’t blameless in the loss. They ran the ball well as Christian McCaffrey and Kaelon Black both averaged over 5.0 yards per carry, but committed four turnovers. These turnovers flipped the momentum of the game in the Falcons’ favor, helping them gain an insurmountable 26–14 lead. Still, it’s unlikely the 49ers will regularly turn the ball over four times in one game. They were also missing their top five receivers—Ricky Pearsall, De’Zhaun Stribling, Mike Evans, Demarcus Robinson and Deebo Samuel—but that was far from the biggest problem as they consistently moved the ball well. It would certainly help the 49ers to add another receiver at the deadline because of the injuries, but their offense remains one of the best in the league when they aren’t recklessly turning the ball over.

Overall, the best case scenario for the 49ers is they use this loss as a wake-up call to retool and improve these flaws during the bye week and become a better team. The worst case is these flaws come back to bite them at an inopportune time, whether it’s keeping them from winning the division or knocking them out of the playoffs.