His ambitious, moody double-disc album The Last Resort was released in 2006 on Poker Flat. The album featured an increased usage of non-electronic instruments, as well as many downtempo and ambient tracks, and it received much critical acclaim. In 2007, Audiomatique released The Trentemøller Chronicles, a double CD retrospective of his non-album work up to that point, including tracks from singles and EPs as well as remixes for Robyn, Moby, and the Knife. Also in 2007, Trentemøller assembled his first live band and performed in the United States for the first time, as well as several European festivals. In 2009, HFN released Trentemøller's Harbour Boat Trips 01: Copenhagen, a mix that primarily contained indie rock and folk rather than electronic music.

Into the Great Wide Yonder, issued on Trentemøller's In My Room label, followed in 2010 and was even more removed from the dancefloor than his first full-length. He continued his successful touring schedule, with his live band featuring up to seven members. Reworked/Remixed, a double CD collecting further remixes released since The Trentemøller Chronicles, arrived in 2011, as did Trentemøller's installment of the LateNightTales compilation series. These releases were followed by 2013's Lost, a song-oriented indie rock-influenced effort that featured guest appearances from Jana Hunter, Marie Fisker, and slowcore group Low. A remixed version of the album, Lost Reworks, appeared in 2014. Fixion, Trentemøller's fourth studio album, followed in 2016 and continued in a similar vein, with its heavily post-punk-influenced lead single "River in Me" featuring vocals from Savages' Jehnny Beth. ~ Rob Theakston, Rovi