Habitat loss is the most likely threat to Phodilus prigoginei.
A Congo bay-owl was almost certainly observed on a tea estate in Burundi in the mid-1970s. Calls of an unidentified owl, structurally similar to that of the Asian bay-owl were heard in Nyungwe forest, Rwanda, in 1990; this forest is at serious (but remediable) risk. In 1996, a small Congo bay-owl was captured in Itombwe, the first positive occurrence in over 40 years.