Recording for the album began at Sarm West Studios in London in mid-1996, with "The Garden Duet" being the first track recorded. While most of The Boatman's Call was recorded at Sarm West, additional recordings and overdubs took place at Abbey Road Studios.

Musically, the album has a sombre and minimalist tone, marking a significant departure for Cave and The Bad Seeds. It shifts away from full-band arrangements and character-based narratives, focusing instead on Cave's solo voice accompanied primarily by piano and a few other instruments. The generally slow tempo reflects the moods of the songs, many of which explore Cave's personal relationships and spiritual yearnings. Some tracks are thought to address the mother of Cave's oldest son, Luke, Viviane Carneiro, in "Where Do We Go Now But Nowhere?" or singer PJ Harvey, with whom he had a brief relationship, as referenced in "West Country Girl," "Black Hair," and "Green Eyes." "Green Eyes" includes a line from "Sonnet 18" by Louise Labé: "Kiss me, rekiss me, & kiss me again."