Neither side did enough to take all three points in a dour contest but the Cobblers will have been happy to pick up only their fifth point of a frustrating campaign.
With strikers Clive Platt and Jacob Blyth on the sidelines, Boothroyd handed Ivan Toney his full debut and the young striker almost crowned it with a goal after a bright start.
Despite seeing his side unable to claim only their second win of the campaign, Boothroyd was happy to get a point.
He said: "We've lost two strikers through injury this week so we're not getting the breaks at the moment.
"Today was all about keeping a clean sheet. We had our chances in the first half when we were on top but we've ground out a result. Now we've got to try and find a way to win games, but starting with a clean sheet is very important.
"We want to win every game we play in but we had to be valiant against a team in good form and who were seventh in the league before the game.
"I thought we were the dominant force for long periods but we know we have to score when we are having our periods of dominance.
"I don't think Morecambe looked like scoring, our centre-backs were excellent and there was only one team that was going to get a goal and that was us."