Babalu-Aye's dread and reverence in his Yoruba homeland once collided directly with colonial law. In the early decades of the twentieth century, British colonial administrators in Nigeria took action against priests of Sopona, the Yoruba name most closely associated with the smallpox aspect of this deity, acting on the suspicion, voiced in colonial reports and by some Yoruba critics, that certain priests deliberately spread infected material to cause outbreaks, extracting payment from frightened communities for the rites believed necessary to lift the affliction they had caused. Colonial ordinances in several Nigerian regions restricted or banned Sopona worship and its shrines on these public health grounds, a rare instance of an African deity's cult becoming the direct target of colonial legislation rather than simply being displaced by missionary conversion.
Historians of Yoruba religion treat the colonial-era allegations with real caution, since they come substantially from an administration with its own reasons to discredit indigenous religious authority, and the true extent of any deliberate spreading of disease by individual priests, as opposed to the ordinary presence of smallpox before vaccination was widespread, is difficult to establish at this distance. What is not in doubt is that the god of epidemic disease briefly became, in a very literal sense, a matter of colonial public health policy, an unusually direct entanglement of religion and state power that shaped how the cult operated in parts of Nigeria for a period, even as devotion to the same figure, chiefly through his identification with Saint Lazarus, only grew stronger across the Atlantic in Cuba during the same century.