Trotta, 19, extended his loan from Fulham this week and the 19-year-old Italian made it six goals in four games for Wanderers with a treble against the Grecians.
The hosts got off to a perfect start by taking the lead after 30 seconds when Anthony McNamee's low cross picked out Trotta and he finished with a first-time shot past goalkeeper Artur Krysiak.
Exeter drew level against the run of play midway through the first half when Danny Coles headed in Chris Hackett's corner at the far post.
But Trotta put the Chairboys back ahead in extraordinary fashion when he took the ball down the left before squeezing a shot past Krysiak from an acute angle.
Guillem Bauza then had a weak penalty saved by Nikki Bull early in the second half before Trotta completed his hat-trick with two minutes to go by sliding a shot underneath Krysiak.
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