The Pilgrims twice led through new signing Greg Smith and the returning Jay Rollins but their National League hosts prevailed after three quickfire goals in the second half.
Wes York grabbed a brace and Liam Hogan also got himself on the scoresheet as the Heed edged a tight and entertaining friendly at the International Stadium.
Boston (4-4-2): Christian Dibble (Michael Emery 80); Trialist, Joe Maguire, Herve Pepe-Ngoma, Courtney Wildin (Joe Burgess 61); Marcus Marshall (Jay Rollins 61), Callum Chippendale, Lewis Hilliard (Liam Adams 74), Jason St Juste; Lamin Colley (Waide Fairhurst 61), Gregg Smith.
Referee: Marc Edwards.
Attendance: 305.