Zamora, whose last goal secured a dramatic play-off final win over Derby County in May and promotion to the Premier League, netted after 13 minutes on Tuesday, with strike partner Charlie Austin grabbing the second.
The win completed a good day for Harry Redknapp, who also secured the signing of Jordon Mutch from Cardiff City.
Steven Caulker again started at the heart of the defence for his new club, partnering Clint Hill, but the pair were hardly troubled by an ineffective Athlone attack.
An early mistake in the hosts' defence gifted QPR the opening goal, Zamora benefiting from a misjudged attempt to clear a cross from the right with an emphatic finish from 12 yards.
Zamora, Caulker and Joey Barton could all have doubled their lead prior to the break, but Austin made no mistake when he was given a sight of goal four minutes before the hour mark.
A crisp passing move released the striker inside the penalty area and he made no mistake with a calm finish into the bottom corner.
More goals could, and probably should, have come Austin's way in the closing 10 minutes but some last-ditch defending kept the scoring down.
QPR therefore had to settle for a two-goal winning margin as they move closer to their Premier League return against Hull City on August 16.