In 2016, for Single-A Lexington, Marte was 6–8 with one save and a 4.21 ERA in 26 games (7 starts), in which he pitched a career-high 107 innings, threw 19 wild pitches (2nd in the South Atlantic League), led the league with 3 balks, and struck out 103 batters. He ranked sixth among South Atlantic League relievers, with a batting average against of .225.
