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As large areas of forest are lost throughout the tropics, prime habitat of many species decline and become fragmented. The island of Borneo is a prime example, with accelerated clearing of forests primarily for oil palm expansion. Borneo is recognized as an important stronghold for the conservation of the sun bear (Helarctos malayanus), but it is unclear how habitat reduction and fragmentation is affecting this frugivore. We used camera traps and sign surveys to understand patterns of sun bear habitat use in a matrix of fragmented forests and extensive oil palm development, which has existed as such for > 15 years: the Lower Kinabatangan floodplain in Sabah, Malaysian Borneo. Within these small forest fragments, squeezed between a major river and oil palm plantations, bears exhibited selection for areas farther from human activity (plantations, river boat traffic, and buildings), and were rarely active during the day, demonstrating both spatial and temporal avoidance of potential human-related threats. They selected large trees to feed and rest, and also exploited adjacent plantations to feed on oil palm fruits. We conclude that even relatively small forest fragments (~ 2000 ha) within large agricultural landscapes can be important for sun bears. Our research highlights the remarkable adaptations this species has employed to persist in a drastically modified landscape.