This data set is a combination of trapping data, tracking data, vegetation/habitat data and data on the gut microbiome composition of wild rodents caught in 4 ha study site in Holly Hill in Wytham Woods, Oxford, UK, from November 2018 to November 2019. Three species of rodents were trapped with Sherman live-traps fortnightly for 12 months: wood mouse (Apodemus sylvaticus), yellow-necked mouse (Apodemus flavicollis) and bank vole (Myodes glaerolus). Upon capture, they were measured, weighted, sexed, aged and a faecal sample was collected from all rodent individuals for microbiome analyses. All rodents were released to their location of capture. First time each individual was captured, they were injected with a permanent subcutaneous Radio-Frequency Identification(RFID)-tag (Passive Integrated Transponder-tag). The tagged rodents were subsequently tracked from February to November 2019 with a set of 120 custom-made tracking devices (loggers). Loggers recorded to time-stamped presence of any tagged individual that passed near it, producing occurrence data suitable for inferring spatiotemporal activity patterns of rodents, such as temporal niches, home ranges and social networks. Bacterial DNA extracted from faecal samples were used to profile their gut microbiome composition. The study area was surveyed for vegetation and microhabitat variation by gathering habitat data of each 10 x 10 m grid square across the 4 ha plot. Data included list of plant species (visible in late May), coverage by the main ground cover types, canopy openness and amount of dead wood in each grid square. This work was funded by a NC3Rs Fellowship to Sarah Knowles, and NERC independent Research Fellowship to Sarah Knowles (NE/L011867/1)