Lubezki frequently collaborates with fellow Mexican filmmaker Alfonso Cuarón. The two have been friends since they were teenagers and attended the same film school at the National Autonomous University of Mexico. Together they have worked on six motion pictures: Sólo con tu Pareja (1991), A Little Princess (1995), Great Expectations (1998), Y tu mamá también (2001), Children of Men (2006) and Gravity (2013). His work with Cuarón on Children of Men (2006), has received universal acclaim. The film utilized a number of new technologies and distinctive techniques. The "roadside ambush" scene was shot in one extended take utilizing a special camera rig invented by Doggicam systems, developed from the company's Power Slide system. For the scene, a vehicle was modified to enable seats to tilt and lower actors out of the way of the camera. The windshield of the car was designed to tilt out of the way to allow camera movement in and out through the front windscreen. A crew of four, including Lubezki, rode on the roof. Children of Men also features a seven-and-a-half-minute battle sequence composed of roughly five seamless edits. Lubezki received further acclaim for his work on Cuarón's Gravity, a 3-D thriller set in outer space.
Most recently, Lubezki collaborated with Terrence Malick on To the Wonder, a romantic drama shot in fall 2010 in Oklahoma, and with Alfonso Cuarón on Gravity, his first entirely digitally acquired film (for which he used the Arri Alexa).