Samuel, who requested a trade in April, did not participate in the practice but did some running on a side field. Because Samuel reported for the minicamp, he is not subject to the fines that go with missing minicamp sessions.
Of more importance, Samuel's presence at the 49ers' training facility for the first time this offseason could be a step in the right direction toward mending the issues that led to his trade request.
Niners coach Kyle Shanahan and general manager John Lynch have been adamant that they don't intend to trade Samuel. Shanahan said at the start of organized team activities in May that he expected Samuel to show up for the minicamp.
After Tuesday's practice, Shanahan said he didn't believe the relationship with Samuel needed much mending and again expressed optimism that the two sides could work something out to keep Samuel in the fold for the long haul.
"I think it's always been all right," Shanahan said. "I know we've gone through the business part of this league and things like that but I don't think the relationship was ever too far away to not get it back to normal and I think we're working on that. Anytime you're away from each other for a while, that's always harder, but it's good to get him back in here and start getting him around the guys again."
When asked whether Samuel has rescinded his trade request, Shanahan said that's a better question for Samuel, who has not been available to the media since his trade request became public knowledge.
Shanahan did, however, say that discussions between the Niners and Samuel's representatives are ongoing and that he and Samuel have had the opportunity to speak in person recently.
"They always talk," Shanahan said. "I love our relationship with Deebo and hopefully that will help us be able to solve this contractually before we get to the season."
While it's still unclear exactly what spurred Samuel to request a trade, he has remained in touch with teammates throughout the process. Quarterback Trey Lance said Tuesday that he and Samuel talk all the time, and left tackle Trent Williams, one of Samuel's closest friends on the team, said Samuel has come to him with questions on the contract negotiation process.
"This is his business, this is his dream, this is his career, I'm definitely not the one to overstep," Williams said. "I try to offer advice if he asks me for some, which he has and we've had good, quality talks and I think that he's grabbing the situation by the horns now and showing how mature he is by showing up, and I think that goes a long way."
Samuel wasn't the only Niner to show up for this week's minicamp after being otherwise absent this offseason. Williams participated in Tuesday's practice, as so did defensive end Nick Bosa.
Like Samuel, Bosa is eligible for a contract extension for the first time in his career as he enters the fourth season of his rookie deal. While the Niners already exercised the fifth-year option on Bosa's contract that would keep him with the team through the 2023 season, Bosa is expected to get a lucrative new deal in the relatively near future.
To that end, Shanahan said contract talks haven't begun yet.
"We haven't been doing that yet with Nick, just that's how both sides are going at it now," Shanahan said. "Not too concerned with it. I fully expect Nick Bosa being here for a very long time."
Also, as expected, quarterback Jimmy Garoppolo is not participating in minicamp. The 49ers excused him from reporting as Garoppolo continues to rehabilitate his surgically repaired right shoulder in Southern California.
"All his rehab is down in L.A., so for him to stop it to come up here for a three-day minicamp doesn't make much sense for him or for us," Shanahan said. "So we want him to stay with his rehab. It wasn't a real risky surgery or anything. It just takes time. So I think the plan still has always been July, but I know there's no concerns with it and he'll be throwing sooner than later."
The Niners still intend to trade Garoppolo once he gets a clean bill of health, though Shanahan said Tuesday that he would expect Garoppolo to report for training camp if he's still on the roster when it opens in late July.
Defensive end Dee Ford has also been excused from this week's minicamp as he figures out his football future. Ford, who has dealt with a back injury for the past couple of seasons, is expected to report for a physical this week.
"I know that we've gotten a good bill of health from his doctors saying how good he is in this spot," Shanahan said. "We're gonna check him out with our physical. [We] do not expect him to be on our team."