Seed dispersal has been an indispensable ecosystem process mediated by biotic and abiotic vectors. Animal-mediated seed dispersal, such as endozoochory has supported plants to sustain and establish in new locations. However, increasing urbanisation may cause the establishment of seed completely dependent on the feces deposition sites. In this regard, this study explores the feces deposition across the eight natural urban forest fragments with varying urbanisation rates in Tokyo-Yokohama, one of the largest urban agglomerations in the world. Paved roads within the forest fragments were surveyed for feces deposition, and the urbanisation rate was estimated for all the studied sites. We found 1381 feces deposited on the paved roads, with the highest in ‘Sagamihara Chuo green space’ (n = 673) and the second highest number of feces in ‘Yokohama National University’ forest area (n = 488). This study revealed a strong influence of urbanisation on feces deposition in the forest fragments. Birds were the most prominent group of animals that deposit feces on paved roads. This study, for the first time, systematically highlights the influence of urbanisation on transforming the seed dispersal service by animals into a potential low service due to seed wastage in feces deposited on paved roads. Urban forest management needs to consider the impact of urbanisation on not just species diversity but also the interactions and services provided by species.