We investigated the terminal electron-accepting pathways and the acetate-oxidizing bacteria in surface sediment (0–5 mm depth) of Aarhus Bay, Denmark, in anoxic slurry and intact core incubations. In the intact cores, oxygen, nitrate, oxides of manganese and iron, and sulfate were all available and likely all used as electron acceptors by the microbial community, whereas microbial iron and sulfate reduction dominated in the slurries. The availability of electron acceptors clearly affected which organisms were labeled by 16S rRNA-stable isotope probing (SIP). Members of the Oceanospirillaceae were identified as 13C-acetate oxidizers in both types of incubations, but bacteria related to Colwellia and Arcobacter oxidized acetate in the intact core, while members of the Desulfuromonadales and Acidithiobacillaceae did so in the slurry incubation. Desulfuromonadales sequences also dominated 16S rRNA gene clone libraries from the highest positive dilution of the acetate-oxidizing most probable number cultures with manganese and iron oxides. Thus, members of Desulfuromonadales are likely important for acetate oxidation coupled to iron and manganese reduction in situ, while the identified Gammaproteobacteria and affiliates of Arcobacter may utilize oxygen, nitrate and manganese oxides. Our study further highlights some of the biases that are associated with the use of RNA-SIP as well as slurry and intact core incubations.