The five-year veteran will skip all of the team's voluntary activities in the final year of his contract, reports CSN Bay Area's Matt Maiocco.
Boone was a no-show for the start of the voluntary three-day minicamp early this week.
A 46-game starter over the past three seasons, Boone is scheduled to earn $3.4 million in 2015.
Although Boone will not skip training camp again this year, per Maiocco, the two sides have yet discuss a contract extension.
In fact, Boone would welcome a trade if it leads to a new contract with another team, Maiocco adds.
That's not an attractive scenario for a rebuilding 49ers team already facing question marks at left guard and center on an offensive line that suffered a considerable dropoff in effectiveness last season.