The Welshman's new side actually got off to a positive start at the Sports Direct Arena and went close to taking the lead in the 16th minute. Shaun Wright-Phillips collected a poor clearance from Ryan Taylor, but saw his curling effort brush the crossbar as it bounced out to safety.
Jay Bothroyd then had another chance for QPR on the half-hour mark, but his right footed effort from the edge of the area flew inches wide of Tim Krul's upright.
Just four minutes later, the home side scored the decisive goal in their first meaningful attack of the match. Leon Best collected possession inside the area before turning past Luke Young and toe-poking the ball beyond the wrong-footed Paddy Kenny in goal.
Bothroyd had QPR's best chance to salvage a point after the break, but he shot straight at Krul after being released by Jamie Mackie.
It is the first time that Hughes has lost his first game in charge of a club.