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Anthropogenic influences caused depletion and subsequent recovery of marine predators, but ecological consequences of altered predator abundance are not well understood. Although many methods are used to study predator diets, methodological biases and logistical challenges preclude robust sampling schemes. We aimed to compare two non-invasive methods: metabarcoding scat-derived deoxyribonucleic acid and hard parts analysis of scat for the Northwest Atlantic grey seal ( Halichoerus grypus (Fabricius, 1791)), a species that rebounded after near extirpation. We hypothesized that metabarcoding would detect a greater diversity and frequency of prey, and that notable differences in diet will be detected since prior studies. Grey seal scat samples ( N = 247) were collected between 2018 and 2019 from Monomoy Island, Massachusetts, USA. Metabarcoding detected greater prey richness on average, with more frequent detections of clupeids (Clupeidae) and flatfish (Pleuronectiformes), whereas hard parts analysis more frequently detected phycid hakes ( Urophycis spp. Gill, 1863). Combining methods increased detections of 13 prey taxa, with 32 prey taxa identified overall. Skates (Rajidae), flatfish, clupeids, and sand lance ( Ammodytes spp. Linnaeus, 1758) were top-occurring prey. Our study highlights the importance of using multiple methods to characterize generalist predator diets using non-invasive techniques and suggests grey seal diet has changed since the early 2000s.