As with other members of the genus, these whales occur almost exclusively in deep waters past the continental shelf edge. Although it is one of the most commonly stranded Mesoplodon species, there have been few sightings at sea, and it is poorly known. De Buffrénil (1995) mentioned that two sightings were north of Scotland and west of the Orkney Islands, in waters several 100 m deep. Hooker and Baird (1999) observed groups of Sowerby's Beaked Whales in the Gully, a submarine canyon off eastern Canada, on four occasions. Sightings were in water depths of between 550 m and 1,500 m.

Ostrom et al. (1993) evaluated the diet of Sowerby's beaked whales, based on isotopic comparisons among northwestern Atlantic cetaceans. They feed on squid and fish, including Atlantic cod (Gadus morhua).