A stupendous strike from Reece Prestedge and a Dwight Gayle penalty condemned Boston United to their first defeat of 2012.
The Pilgrims were deservedly beaten by in-form Bishop's Stortford after turning in another disappointing home display.
Boston were second best during the first half and were fortunate to be level at the break.
But United's luck ran out just two minutes into the second half when Prestedge curled home a wonderful shot from more than 20 yards.
Like during Saturday's 1-1 draw with Blyth Spartans, the Pilgrims didn't come alive until the final quarter.
Player-manager Jason Lee was denied by Stortford keeper Jordan Archer while Danny Sleath saw an effort headed off the line.
But Stortford were dangerous on the break and they extended their lead in added time when Gayle rattled home a penalty.
The Pilgrims must now regroup ahead of Saturday's FA Trophy tie at Dartford FC.