With snow falling throughout Tuesday night's League Two encounter at The Rec, Daniel Lopez swept the Shots ahead from close range in the second minute but Chris Hackett levelled from the spot before Clarke Carlisle headed the Cobblers in front before the break.
It was enough to secure Northampton only their third away win this season, and Boothroyd knows his side need to keep taking points away from Sixfields.
"This was a step in the right direction but we have to keep improving our away form," said Boothroyd.
"I just think we've let ourselves down away from home. Five of our next six games are away so we'll need to step it up.
"This was a great victory for us in difficult conditions. But nothing gets won in the winter. It's all about the last day, that's when the prizes are given out.
"We've got a long way to go and we're nowhere near as good as we can be, but I thought we deserved it. We took our chances but we maybe should have got another goal.
"I've played games on icy pitches before and in foreign countries when the heat is stifling, but never with so much snow on the pitch. But the players got on with it."