Globally, the use of agricultural fields by waterbirds has increased, resulting in conflicts with farmers. Designing effective management strategies to resolve these conflicts requires understanding the species' resource use. Dietary analyses can shed light on the extent of consumption of agricultural crops and surrounding natural resources, as well as the potential relationship between diet and an individual's body condition and ultimately its fitness. We examined the dietary composition of the tropical magpie goose Anseranas semipalmata, seasonally utilising a mixed natural-agricultural landscape of northern Australia. We used DNA metabarcoding of intestinal contents from hunted geese to reconstruct individual diets and evaluated body condition from morphometric measurements. We compared the relative contribution of agricultural and natural foods to dietary composition, and investigated how this contribution varied spatially, temporally and among individuals that differed in body condition. We found that geese consumed both agricultural and naturally occurring plants assigned to at least 35 taxa. The most frequent and abundant taxa belonged to three families: Poaceae (grasses), Cyperaceae (sedges) and Anacardiaceae (mangoes). Dietary composition varied substantially among sampling sites and over time but not with body condition of geese. Synthesis and applications. We used a novel approach to investigate the diet of a waterbird perceived as problematic across an agricultural landscape in tropical Australia. We showed that individuals forage opportunistically, and that agricultural crops, while eaten, may not represent an essential part of geese diet across the study region. The knowledge acquired provides new insights into the species' foraging ecology offering clear alternatives for mitigating goose–agriculture interactions. Providing disturbance-free alternative foraging areas or minimising the attractiveness of targeted agricultural fields (e.g. shorter grass, alternative ground cover) may alleviate crop consumption while benefiting the species' long-term conservation. While also highlighting the limitations of DNA metabarcoding, our dietary study emphasises the potential of this methodology to improve our understanding of crop damage by wildlife, allowing effective evaluation of management requirements.