ABSTRACT Microbes found in nectar and dispersed by animal visitors can mediate pollination and host fitness. While previous studies have characterised floral nectar microbiomes and their effects on invertebrate pollinators, fewer studies have focused on vertebrate pollinators, especially outside of the Northern Hemisphere. In Aotearoa New Zealand, vertebrates, such as birds and bats, are critical pollinators for many native plant species. Here, we present nectar microbiome profiles for two endemic, vertebrate-pollinated plant species in Aotearoa New Zealand, wharariki, mountain flax (Phormium cookianum), and pua o te Rēinga, wood rose (Dactylanthus taylorii). We used vertebrate exclusion treatments and camera traps to monitor visitation. Camera trap footage revealed silvereye (Zosterops lateralis), ship rat (Rattus rattus), and possum (Trichosurus vulpecula) visitation. We detected shifts in microbial species turnover in wood rose and varying relative abundances of fungal and bacterial taxa across the vertebrate exclusion treatments for both mountain flax and wood rose. However, we did not detect strong effects on floral nectar microbiome community composition or richness. Future work should move beyond profiling the microbial communities and identify fitness consequences and pollination outcomes, which could affect conservation and management decisions.