Endangered cranes migrate to the Demilitarized Zone in Korea in search for habitat and food during winter. While cranes have the potential to influence soil biogeochemical processes via dropping, foraging, and walking, few studies have investigated ecological roles of migrating birds in the new habitat. Here, we explored how cranes alter resource landscape (the amount and quality of carbon) and microbial community in soil. We set up control (fenced, no crane access) and treatment (free crane activities) plots (n = 6, respectively) in a rice paddy, and collected soils at 0-15 cm three months after the crane migration. Soils were tested for total carbon, total nitrogen, water extractable organic carbon, and Diffuse Reflectance Infrared Fourier Transform Spectroscopy, along with microbial parameters (biomass, respiration, community composition). The wintering crane activity significantly increased total carbon and nitrogen contents, but decreased the ratio of CH (aliphatic) to COO (carboxylic) in soil. Also, both microbial biomass and respiration was greater in soils under crane activities. Bacterial and fungal community composition differed with or without crane activities, with treatment soils harboring more diverse microbial communities. Our results demonstrate that crane migration created a distinct system with altered resource landscape and microbial community, highlighting beneficial effects of migratory cranes on the soil biogeochemical processes in rice paddies. This study may help encourage more farmers, local governments, and the public to participate in crane conservation campaigns targeted at rice fields.