A goal in each half from Braintree forward Aryan Tajbakhsh gave Town their first defeat of pre-season.
Town manager Paul Hurst named a strong starting XI as Braintree took the lead on 12 minutes when Tajbakhsh finished comfortably from 15 yards.
The National League side doubled their lead just past the hour when Tajbakhsh bent a superb free-kick around the wall and into the bottom corner.
The blues made wholesale changes when they were 2-0 down, but Town were unable to threaten in the closing stages and fell to a defeat in their second pre-season game of 2018-19.
Next up for Town is against Crawley at East Grinstead on Tuesday evening.
Town: Gerken (Wright 65), Emmanuel (Woolfenden 46), Spence (Cotter 65), Chambers (c) (Ndaba 65), Kenlock (Webber 65), Skuse (Dozzell 65), Downes (Nydam 46), Ward (McKendry 65), Sears (Folami 65), Waghorn (McGavin 65), Roberts (Drinan 65).