Ferric salt dosing is widely used to mitigate sulfide and methane emissions from sewers. In gravity sewers with sediments, responses of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) residing in different zones to Fe3+ dosing strategies still remain unknown. In this study, we investigated the changes in behavior of SRB and MA in different depths of sewer sediment using laboratory-scale sewer sediment reactors with different Fe3+ dosing strategies (different instant dosages and frequencies). All Fe3+ dosing strategies examined efficiently suppressed sulfide concentration for a short time, but the control mechanisms were different. When a low-dosage, high-frequency Fe3+ dosing strategy was employed, Fe3+ could not penetrate into the sewer sediment, therefore, the abundances of SRB and MA in all zones of sewer sediment did not change substantially. As a result, the active sulfide-producing and methane-producing zones kept unchanged. Sulfide was controlled mainly via chemical sulfide oxidation and precipitation, and methane formation was not influenced. In contrast, when a high-dosage, low-frequency Fe3+ dosing strategy was used, the SRB activity in the upper layer of the sewer sediment was nearly fully suppressed according to the down moving zones of sulfide production (from 0-5 mm to 20–25 mm) and lower sulfate reduction, in which sulfate reduction decreased by 56% in the long-term trial. The generated sulfide was further removed via chemical sulfide oxidation and precipitation. This strategy also significantly suppressed MA activity (21% reduction in methane production). However, considering a long-term satisfactory sulfide control, a low operational cost and less sediments deposited in gravity sewers, a low-dosage, high-frequency Fe3+ dosing strategy would be a more cost-effective solution for sulfide control in gravity sewers with thin (<20 mm) or thick (>20 mm) sediments if methane mitigation does not need to be taken into account.