[9] In 2013, Lowery wrote, directed and edited his second feature film, Ain't Them Bodies Saints, starring Casey Affleck and Rooney Mara.

[11] Lowery has said that he drew from great directors and their works for this film, citing Claire Denis's 35 Shots of Rum,[12] Robert Altman's McCabe & Mrs. Miller,[13] and Paul Thomas Anderson and David Fincher as influences.

[14] In addition to having edited films such as Amy Seimetz's Sun Don't Shine and Shane Carruth's Upstream Color,[15] Lowery co-wrote Pit Stop with director Yen Tan.

[20] In November 2016, it was announced Lowery had shot a new film, A Ghost Story, over the summer with Rooney Mara and Casey Affleck as a secret project.

[21][22] Lowery next directed the 2018 drama film The Old Man & the Gun, starring Robert Redford as bank robber, Forrest Tucker, and Casey Affleck.

[23] Lowery followed up The Old Man and the Gun with the medieval fantasy The Green Knight which stars Dev Patel, Alicia Vikander, Joel Edgerton, Barry Keoghan, Ralph Ineson and Sean Harris.

[31] After working with Disney on Pete's Dragon, Lowery signed on to direct a live-action adaptation of their 1953 animated film Peter Pan in April 2016.