Wilson's Storm-Petrel has "an extremely large range" and a very large population. Consequently the IUCN Red List status of Wilson's Storm-Petrel is assessed as of Least Concern.

Though the population of Wilson's Storm-Petrel is stable, introduced predators at nesting sites such as rats and cats still pose a problem at some lower latitude sites. An additional risk is posed by heavy metals and organochlorines, which may accumulate in the birds' tissues (Croxall et al. 1984). Ingestion of plastic is a major concern, as a high proportion of adults and prefledged chicks have had been reported to have plastic in their stomachs (Moser and Lee 1992). Incidents of birds feet getting tangled in fishing mesh or nylon lines also occur (Moore 1992).

Quillfeldt (2001) reports lower breeding success after winters with low sea ice, reflecting the effects of climate change on this species.