Hodddesdon had a goal disallowed for offside early in the game before they were surprised by Town’s 18th minute lead.
John Shittu put in a good cross from the left for Jacob Joseph Hukin to fire in from close range.
Hukin almost provided a second, crossing from the right only for Jay Fattorusso to head against the post with the keeper beaten.
But Hoddesdon increased their tempo in the second half, forcing Town to defend in numbers.
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The Lilywhites’ hard work paid off when Ben Andreos levelled in the 81st minute from a corner and, soon afterwards, substitute Harry Mavromatis beat Matt Jones with a 20-yard shot to secure a win – meaning Town came back from Lowfield with nothing for their efforts.
It was another encouraging display and youngster Louie Dillon created a lot up front.
In the same week, Town made an early exit from the Challenge Trophy at Division One side Southall, going down 1-0.
A goal in the first 15 minutes proved to be enough in a game in which Town were missing some regulars.
They were guilty of misplaced passes in the first half but gave a much improved display after the break.
Youth players Fraser Maidment and Dillon were both introduced at the break and both gave a good account and created fair openings.
Ampthill had much the better of the second half but found the home back four an uncompromising unit, although on another night one or two of the half chances they created might have had greater fortune.
Town are still without an SSML Premier Division win going into October and have no game scheduled this weekend.
They travel to Biggleswade United next Tuesday before a home match with St Margaretsbury.