Monarch butterflies, Danaus plexippus L., in western North America are undergoing a seemingly volatile shift in seasonal population dynamics which includes novel winter-breeding on non-native milkweed in urban areas of northern California. The survival, viability and outcome of monarch pupae in the wild was evaluated for the first time by regular monitoring of a cohort of 104 pupae in a San Francisco managed urban landscape during the winter of 2021/22. Seventeen pupae were destroyed by landscaping activities. Almost half (49.4%) of the remaining pupae eclosed, with ∼ 70% likely infected with varying levels of the protozoan parasite Ophryocystis elektroscirrha (OE). A third of the pupae (32.2%) died of unknown causes, while the remainder (18.4%) disappeared, presumed predated. Two monarchs were killed while eclosing, by European paper wasps, Polistes dominula (Christ, 1791). Microscopic examination of pupal exuviae for spores of OE appeared to be a satisfactory proxy for microscopic examination of butterfly abdomens, in determining the presence/absence of infection. The developing importance of winter breeding in western monarch ecology necessitates modifications to conservation guidelines that enhance the survival of immature stages, acknowledging the role of non-native milkweeds while minimizing parasite infection.