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Logging has been operated throughout Bornean tropical forests that harbor diverse fauna species. We examined the responses of ground-dwelling wildlife to logging intensity in two certified forest management units under the same climate and vegetation in East Kalimantan, Indonesia, in 2012–2016. A total of ten and 13 circular plots with a diameter of 1 km were established respectively, and 10–18 camera points were distributed randomly in each plot to record wildlife for two years. A total of 41 species of medium to large-sized terrestrial wildlife were recorded in the two management units. Canonical Correspondence Analysis (CCA) was performed to examine the response of wildlife community to the logging influences with the following three variables: forest intactness (as a surrogate of tree-species composition), above-ground carbon (as a surrogate of forest structure), and distance to the nearest village to represent hunting pressure. Forest intactness was the strongest factor affecting the assemblage of wildlife species in both management units, suggesting that changes in tree-species composition due to logging were a decisive factor influencing animal assemblage. Poisson Generalized Linear Model (GLM) was employed to examine the response of each species to forest intactness in each management unit. We found that eight out of the 32 tested wildlife species responded to forest intactness consistently between the two units, while the other species responded more individualistically. We suggest that consistent responses of several species, as well as individualistic responses of the other species to the changes of tree-species composition, determine the animal assemblage in logged-over Bornean rainforests. Sustainably managed logged-over forests in Borneo are a habitat for diverse wildlife community and therefore also require attention for biodiversity conservation.