The 21-year-old made 25 appearance on loan to Argyle from the Wanderers during last season.
He missing out on playing the League Two play-offs for Argyle because of the terms of his loan deal.
But, now his Bolton contract has expired, he has returned to Home Park on an undisclosed-length deal.
Following goalkeeper Vincent Dorel's new contract, Pilgrims boss Derek Adams now has 18 first-team players under contract for the 2016-17 season, which starts on 6 August.
Find all the latest football transfers on our dedicated page.
Plymouth Argyle make their 10th summer signing by bringing in former loan midfielder Oscar Threlkeld after he was released by Bolton Wanderers.