Manningham struggled with injuries throughout the campaign, managing just six appearances for the 49ers and recording nine receptions for 85 yards.
"It was frustrating, but it was a learning experience also. When I got back I couldn't do what I wanted to, I knew I needed a little bit more time," Manningham said in a press release.
"It's coming along and I just have to work on getting stronger and getting my strength back and trusting it more. I'm doing good; it's getting stronger."
Manningham spent four years with the Giants, helping them to Super Bowl success in 2011 before joining the 49ers.