Differences in the diets of urban and rural avian predators could indicate potential niche vulnerability in a particular habitat. This study compares the core-isotopic niche areas and diet disparity of a declining peri-urban Verreaux’s Eagle Aquila verreauxii population with a stable rural population in South Africa. In addition to stable isotope analyses, the diet of the peri-urban Verreaux’s Eagles was investigated using camera trap footage of prey delivered during the nesting season. Dominant prey consisted of species with a mixed diet of plants with a C3 and/or C4 photosynthetic pathway (browsers and grazers). Rock hyrax Procavia capensis contributed 60% of the total diet composition, scrub hare Lepus saxatilis 26% and Helmeted Guineafowl Numida meleagris 22%. The core-isotopic niche area for each population was calculated using bulk carbon (δ13C) and nitrogen (δ15N) stable isotope values chronological measured along the length of 18 feathers from 21 nests. The isotopic niche of the rural eagle population revealed that they consume prey from multiple trophic levels with a C3-plant-dominated prey base (browsers), likely including small carnivores. In contrast the isotopic niche of the peri-urban Verreaux’s Eagles correlated with the mixed mammalian and avian food-niche determined from camera trapping, confirming that the peri-urban population mainly hunted three abundant species that are all narrowly associated with modified human habitats. The decline in the Magaliesberg Verreaux’s Eagle population is, therefore, unlikely to be due to constraints in their dietary niche, as raptors benefit from the diversity and abundance of human-commensal prey associated with the peri-urban habitats.