Striker Simone Akinola gave Iron the lead after 15 minutes, with Michael Cheeks doubling the lead, just after the half-hour mark.
Steve Cawley curved an excellent free-kick home to pull a goal back for the Beachboys.
Lee Barnard secured Iron's latest victory in pre-season, as he converted from the penalty spot in the final stages.
Town travel to Bishop's Stortford in a pre-season friendly on Saturday.