Coral ingestion by crown-of-thorns starfish (CoTS) is an important cause of coral reef degradation, although the impacts of CoTS feeding on coral-associated communities are not well understood. Therefore, in this study, we analyzed the zooxanthellae density (ZD), bacterial community composition, and microbial-metagenomic functional capacities associated with Pocillopora corals in healthy portions and feeding scars, following CoTS feeding. The ZDs were significantly lower in the feeding scars, and the ZD-loss rate was 92.05% ± 2.12%. The relative abundances of bacterial communities associated with corals after CoTS feeding changed significantly and were almost completely reorganized at the phylum and genus levels. Analysis of the microbial metagenomic-functional capacities showed that numerous physiological functions of the coral-bacterial holobionts in the feeding scars were diminished, including amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, membrane transport, signal transduction, and cell motility. Compared with the healthy portions of Pocillopora corals, the abundances of potentially pathogenic bacteria in the corals of feeding scars significantly increased, whereas those of beneficial bacteria significantly decreased. Our research showed that coral-zooxanthellae holobionts were destroyed directly by CoTS, and our findings imply that the large increase in potentially pathogenic bacteria in feeding scars could threaten the long-term health of Pocillopora corals.