49ers GM John Lynch envisioning long-term future with Jimmy Garoppolo

He hasn't made it into a game for them yet, but the 49ers say Jimmy Garoppolo, center, checks all the boxes for a franchise quarterback. Stan Szeto/USA TODAY Sports

SANTA CLARA, Calif. -- San Francisco 49ers general manager John Lynch will leave the decision of when to start quarterback Jimmy Garoppolo for the first time in the hands of coach Kyle Shanahan.

But in the few weeks Lynch has gotten to know Garoppolo since the Niners traded for him on Halloween, he has seen nothing to deter him from the idea that Garoppolo can and will become the team's franchise quarterback.

In a wide-ranging 40-minute discussion with a handful of Bay Area reporters on Tuesday, Lynch was more forceful than he has been about how he and the Niners view Garoppolo's future with the team.

"He's going to be our guy, you know?" Lynch said. "We feel like we've got a great quarterback room. You watch the way C.J. Beathard played the other day, he looked like he could be the guy. I think it's a good issue, and we also realize that we have got to grow around them and we've got to continue to put pieces in place, and we will."

Lynch declined to say whether the Niners have already engaged agent Don Yee, one of Garoppolo's representatives, in contract extension discussions. He did, however, acknowledge that the 49ers have been in touch with the agents for some of their players who are headed for free agency.

Garoppolo is scheduled to be an unrestricted free agent this offseason, but the 49ers have also made it clear they are aware that they have options when it comes to retaining his rights.

Some alarm bells went off recently when Lynch said in a radio interview that Garoppolo could be seen as a trade "chip" in a worst-case scenario after the team acquired him. Lynch made it a point to clarify that comment when asked if he could see a scenario in which the Niners would trade Garoppolo after the season.

"That probably was a stupid thing to say because people take that and [run]," Lynch said. "I think what the point was, Kyle said, 'We love this guy,' but [that comment about the chip] was a throwaway. If you just took away our feelings for him and said, 'If we were to do this for that [trade],' then it's a good decision based upon that alone. So that is not at all how we think.

"We really, genuinely believe that this guy has got the makings of a guy who could be our guy for years to come. That's all got to come to fruition on the field and all that, but that was kind of a throwaway line that got a lot of attention."

Of more importance for Garoppolo's long-term future with the Niners is what Lynch and Shanahan have seen from him since he arrived. All parties were hesitant to declare Garoppolo the face of the franchise on the day he was acquired, but a big reason for that was the relative lack of familiarity that existed on all sides.

Now, the 49ers are invested enough in Garoppolo and Beathard that Lynch acknowledged Tuesday that the team's scouting staff has scaled back its efforts in looking at college quarterback prospects.

Garoppolo has been in the building for nearly a month and had a chance to show his work ethic, interact with his teammates and coaches and display his physical ability on the field. According to Lynch, Garoppolo has checked all of those boxes in a positive way, whether it be how well his teammates have embraced him, his quick release and accuracy throwing the ball or his willingness to stay around the facility and put in extra work.

So while Lynch and the Niners still want to see that manifest in a game, they have gotten enough of an idea of what he brings to feel confident in him.

"The work ethic, the intangibles and the skill set, like I said, of course, with as little as he's played, some of this is projection and we understand that," Lynch said. "We felt very comfortable with Kyle having studied him in college, we having studied him together this offseason, you can just talk about the games he's played, the preseason and such. There's a lot that we like."

In the short term, questions still abound about when Garoppolo will make his 49ers debut. He spent as much of his bye week as the league allows at the team facility studying with Shanahan and quarterbacks coach Rich Scangarello. Most of that time was spent circling back to the basics of the offense rather than focusing on small pieces of a weekly game plan.

Shanahan will ultimately make the call whether Garoppolo or Beathard starts this week, a decision that once seemed academic but might have been altered a bit by Beathard's strong performance in leading the Niners to their first win of the season against the Giants.

"C.J. playing the way he played last week, we think before that even, some adverse situations, the way he handled himself, gives us an opportunity to kind of continue to really -- we're trying to accelerate the growth, but we don't want to rush it," Lynch said. "But it gets a little better and gets a little more comfortable with each given day. He's working at it extremely hard."

Regardless of when Garoppolo gets his opportunity -- and at this point it seems to be more a question of when rather than if -- Lynch will join many others in their enthusiasm to see how he performs.

For it's the final and biggest piece in determining how the Niners and Garoppolo proceed in the future.