Urbanisation alters natural habitats and impacts biodiversity, including key ecological functions such as animal-mediated seed dispersal. The novel habitats create environmental heterogeneity changing animal’s ability to disperse seeds. This study evaluated how urbanisation indicators and habitat heterogeneity influence endozoochorous seed dispersal by raccoon dogs (Nyctereutes procyonoides), an urban adapted omnivore in the urban forest fragments of Tokyo metropolitan area. We surveyed the latrines of raccoon dogs in 19 urban green spaces and identified 67 plant species, predominantly native, dispersed by these mammals. It was found that the urbanisation rate (built-up area) significantly influenced plant species found in feces, while artificial light and population density showed no significant effects. Habitat heterogeneity evaluated using buffer zones of varying radius, negatively impacted species richness, and seeds in the feces, with larger spatial scales (700-1000 m) showing more pronounced effects. Despite urbanisation’s homogenising pressures, raccoon dogs predominantly dispersed native plant species, maintaining the stability of the local ecosystem. The most important species for raccoon dogs at the sites were Morus australis and Aphananthe aspera. However, the mismatch between the species in feces and the local vegetation at the sites suggested a broader feeding behaviour. This highlighted the dual role of urban forest fragments in supporting dispersers while mitigating seed dispersal efficiency due to fragmentation and human intervention. Our findings emphasise the need to integrate urbanisation indicators and heterogeneous habitats with conservation strategies to sustain ecological functions. This work underscores the importance of urban-adapted raccoon dogs in fostering biodiversity and ecological processes while facing the challenges of urbanisation.