Urbanization affects biodiversity and essential ecological functions, such as animal-mediated seed dispersal. Novel urban habitats introduce environmental heterogeneity that alters the effectiveness of animal-mediated seed dispersal. Despite growing urbanization, the additive effect of urban indicators on habitat diversity in shaping animal-mediated seed dispersal by urban mammals remains poorly understood. Hence, this study examined the influence of urban indicators and habitat diversity on endozoochorous seed dispersal by urban-adapted raccoon dogs within urban forest fragments of the Tokyo metropolitan area. We surveyed raccoon dog latrines across 19 urban green spaces and identified 66 plant species in its feces with most of them primarily native. The most frequently dispersed species were Morus australis and Aphananthe aspera. However, discrepancies between plant species found in the feces and those present in local vegetation suggest a broader foraging range beyond the study sites. The results showed that presence of more built-up area, significantly increased plant species richness in feces. The additive effect of built-up areas and habitat diversity increased endozoochory at larger scales. This underscores the role of seed dispersers in maintaining plant diversity in urban forest fragments, where increasing habitat diversity at large scales supports more plant dispersal. Our findings highlight the importance of native plants in endozoochory, which supports their conservation by dispersing them. This study reinforces the ecological importance of urban-adapted raccoon dogs in maintaining biodiversity and ecological processes despite the challenges posed by urbanization