The San Francisco 49ers secured backup quarterback plans on Monday as free agency kicks off.

Backup quarterback Brandon Allen agreed to re-sign with the team, which NFL Network’s Ian Rapoport first reported on Monday. Allen signed with the 49ers in 2023 and spent the season as third on the depth chart.

His career started with the Jacksonville Jaguars as a sixth-round NFL Draft pick in 2016. Allen bounced around the league at first, but he found opportunities with the Denver Broncos in 2019 and Cincinnati Bengals from 2020 to 2022.

With the Broncos, Allen started three games and went 1-2 as he threw for 515 yards and three touchdowns versus two interceptions. His time in Cincinnati went better amid his 61.5% completion rate for 1,096 yards and seven touchdowns versus four interceptions in relief of starter Joe Burrow.

San Francisco bringing back Allen could signal that fellow backup Sam Darnold is on the move for free agency. A former No. 3 pick in 2018, Darnold looks poised to seek another starting job after he sat behind starter Brock Purdy for the year.

𝗕𝗿𝗲𝗮𝗸𝗶𝗻𝗴: The #49ers are re-signing QB Brandon Allen, per @RapSheet pic.twitter.com/oE64lFZwXh

— Dov Kleiman (@NFL_DovKleiman) March 11, 2024

Darnold also signed with the 49ers as a free agent in 2023 for a one-year, $4.5 million deal. Allen meanwhile had a one-year, $1.23 million deal with the team.

San Francisco faces a challenging salary cap situation this offseason, and the organization will need to make adjustments amid $7.43 million over the salary cap. The 49ers already lost captain Arik Armstead due to his refusal to take a pay cut, and fullback Kyle Juszczyk likewise received a pay cut request according to Pro Football Network’s Adam Caplan.

The Niners had one success in cutting costs as linebacker Fred Warner restructured his contract according to The Athletic’s Matt Barrows.

Brandon Allen: ‘This System Works Well’

Allen expressed his comfort with the 49ers offense as early as training, which bodes well if he becomes the main backup in 2024.

“This system works well for quarterbacks who can just be accurate and play on time,” Allen told NBC Sports Bay Area at camp in 2023.

Allen looks poised to become the No. 2 quarterback, but the 49ers could make another inexpensive signing or pick a late-round quarterback in April’s draft. This year’s draft has a deep field of prospects and the 49ers could tab the likes of Notre Dame’s Sam Hartman or Tennessee’s Joe Milton Jr.

If the 49ers draft a quarterback, Allen gives the team another veteran mentor for a rookie. In addition, the Niners will need Allen if Purdy goes down with an injury.

San Francisco had enough confidence in Allen to serve as the emergency quarterback in the postseason. The 49ers had to dig that far into the roster before in the 2022 NFC Championship Game against the Philadelphia Eagles when Purdy sustained an elbow injury.

Niners Kept Brandon Allen Instead of Trey Lance

San Francisco arguably showed more confidence in Allen than former No. 3 pick Trey Lance last year when the team traded Lance to the Dallas Cowboys in August 2023. The 49ers then kept Allen for the final 53-man roster.

Pro Football Talk’s Mike Florio explored the situation and noted the “suspicion in some circles” that Lance was headed for fourth string. Lance spent the 2023 season as the Cowboys’ third quarterback.