Benthic food-web structure and organic matter (OM) utilization are important for marine ecosystem functioning. In response to environmental changes related to the ongoing climate change, however, many benthic species are shifting their ranges to colder regions, which may lead to altered community composition, but it remains largely unknown how it will affect ecosystem functioning. Here, stable isotope analysis was used to study benthic OM utilization and food-web structure and to assess whether their spatial patterns reflect today's community differentiation among biogeographic regions and depth zones. Benthic fauna and OM mixtures were collected from two depth zones (100–150 m vs. 200–250 m) within a temperate, two sub-Arctic, and an Arctic fjord along a latitudinal gradient (59–78° N) that was used as a space-for-time substitution to assess the impact of climate change. Our results showed that Arctic and temperate communities are functionally different. Arctic communities were characterized by a strong resource partitioning among different feeding types, irrespective of depth zone. In contrast, all feeding types in temperate communities seemed to rely on sedimentary OM. The sub-Arctic presented a transition zone. In the sub-Arctic, shallower communities resembled Arctic communities, suggesting a functional transition between temperate and sub-Arctic regions. Deeper sub-Arctic communities resembled temperate communities, suggesting a functional transition between the sub-Arctic and Arctic regions. This implies that the regions north of the current transitions (deep Arctic and shallow sub-Arctic) are most likely to experience functional changes related to an altered OM utilization in benthic food webs in response to climate change.