Mesophotic rocky reefs are stable environments for animal forests to establish and grow. These systems, largely characterised by sponges and other sessile invertebrates, provide essential food, habitat and ecosystem services for a range of economically and ecologically important taxa. Anchor scour from shipping is highlighted as a threat to the marine estate, yet the biological impacts remain a significant knowledge gap. Increases in world trade and uncertainty from global crises pose a poorly characterised threat to critical marine habitats essential for ocean health. We quantified the morphotype richness and relative abundance of animal forests in recently anchored locations and compared these to ‘anchor-free’ reefs to assess the impacts to biota on temperate mesophotic reefs. We examined 10 taxa from 4 phyla to determine biota most at risk. Our analysis revealed striking impacts to animal forests exposed to anchoring with three-fold declines in morphotype richness and five-fold reductions in relative abundance, along with marked compositional shifts, relative to those that were anchor-free. Six taxa exhibited strong negative responses to anchoring, one was indifferent and the remainder were too patchy in abundance to assess. Our research indicates that anchoring on reefs leads to the substantial removal of biota and impacts to biodiversity.