Lee Collins poked home 20th-minute opener when he raced on to Darren Carter's free-kick - Northampton's first away goal of the season.
Stuart Dallas made sure of Northampton's second league win of the season with 16 minutes remaining as he scored a fine solo goal to double the visitors' lead.
Matt Duke made a fine save to deny promotion-chasing Wimbledon's Harry Pell an injury-time consolation and Boothroyd hopes this is where the Cobblers' season picks up.
"We've got to build on this, Wimbledon were in fantastic form and it's a good result for us," he said.
"We know we've had a bad start, but I've been really, really pleased with the last two games.
"We stuck at it and we were very, very solid. If anything we could've scored more goals, the opportunities were there.
"They're where they are in the league for a reason, and we knew it would be tough to beat them, and two clean sheets in a row make this a massive, massive result.
"When we're away from home we're there to frustrate and to upset. Our away record in my time hasn't been great, but our home record has been fantastic.
"If we can get it back on track, and pick up the odd result like this, in the next 10 games we'll be a lot happier. I'm not getting too excited, but I'm genuinely very, very happy."