Changing climatic conditions coupled with other anthropogenic stressors can cause irruptions of native species, with potentially similar widespread effects to those caused by range-extending or invasive species. Emerging evidence suggests that the native subtropical sea urchin Centrostephanus rodgersii is increasing in abundance throughout northeastern Aotearoa New Zealand; however, long-term population trends and associated impacts across multiple rocky reef habitats are poorly understood. Long-term rocky reef monitoring and resurveys of historical sites, coupled with field and lab-based experiments were used to assess if C. rodgersii populations have increased over decadal time spans and quantify associated impacts on kelp forest and low light, sessile invertebrate dominated rock wall habitats in the region. We found significant long-term increases in C. rodgersii densities within both habitats, along with the emergence of associated urchin barren habitat and declines of habitat forming macroalgae and invertebrates. Laboratory-based feeding experiments and stable isotope analysis supported these findings, with C. rodgersii exhibiting an omnivorous diet, readily consuming a variety of algae and sessile invertebrate species. Observed increases in abundance are likely associated with long-term ocean warming and low predator numbers. This highlights the novel and unprecedented threat that C. rodgersii poses to multiple rocky reef habitats in New Zealand.