Marrow of the Spirit marked a change in record labels for Agalloch. Their first three full-length albums and EPs were released by The End Records, but after their contract was completed with the release of Ashes Against the Grain in 2006, the band opted not to renew it. Marrow of the Spirit was released by Profound Lore Records, which had also released the first two Agalloch albums on vinyl in 2005. It was the first album to feature Aesop Dekker (of Ludicra) on drums, replacing Chris Greene.
The band felt that their previous album, Ashes Against The Grain, sounded too polished, and opted for a more raw sound for Marrow of the Spirit, saying that it felt more "alive and real." The album thus was recorded entirely on vintage analog equipment. Recording took place at Audible Alchemy Studios in Portland, Oregon with Steven Wray Lobdell producing.
On October 29, 2010, the track "The Watcher's Monolith" was released on the music website Stereogum accompanied by an interview with John Haughm. The track "Ghosts of the Midwinter Fires" was released on November 1.