Migratory species that cross geopolitical boundaries pose challenges for conservation planning because threats may vary across a species' range and multi-country collaboration is required to implement conservation action plans. The lesser long-nosed bat (Leptonycteris yerbabuenae) is a migratory pollinator bat that was removed from the Endangered Species List in the United States in 2018 and from threatened status in Mexico in 2013. The seasonal ecology and conservation status of the species is well understood in the core part of its range on mainland Mexico and in the southwestern United States, but relatively little is known about the species on the Baja California peninsula in northwestern Mexico, a part of its range range separated by the Gulf of California. We studied the seasonal ecology of lesser long-nosed bats on the Baja peninsula at 8 focal roosts along a 450-km north-to-south transect to test hypotheses about migratory or residential status of the species on the Baja peninsula. We provide evidence of an extensive population of lesser long-nosed bats on the Baja peninsula that is primarily seasonally migratory and includes 2 mating roosts with males on the southern part of the peninsula. Seasonal ecology of lesser long-nosed bats was closely associated with the flowering and fruiting season of the cardón (Pachycereus pringlei), the dominant columnar cactus on the peninsula. However, we discovered that some female lesser long-nosed bats arrive and give birth at southern roosts in mid-February, about 2 months earlier than other migratory populations in more northern Sonoran Desert habitats. We documented the loss of nearly a third of the known maternity roosts during the study, demonstrating that action to protect key roosts remains a high priority. Migratory pollinators are particularly vulnerable to climate and land-use changes and we recommend continued monitoring and research to guide effective range-wide conservation of the species.