To evaluate the impact of invading seagrass on biogeochemical processes associated with sulfur cycles, we investigated the geochemical properties and sulfate reduction rates (SRRs) in sediments inhabited by invasive warm affinity Halophila nipponica and indigenous cold affinity Zostera marina. A more positive relationship between SRR and belowground biomass (BGB) was observed at the H. nipponica bed (SRR = 0.6809 × BGB − 4.3162, r 2 = 0.9878, p = 0.0006) than at the Z. marina bed (SRR = 0.3470 × BGB − 4.0341, r 2 = 0.7082, p = 0.0357). These results suggested that SR was more stimulated by the dissolved organic carbon (DOC) exuded from the roots of H. nipponica than by the DOC released from the roots of Z. marina. Despite the enhanced SR in spring-summer, the relatively lower proportion (average, 20%) of acid-volatile sulfur (AVS) in total reduced sulfur and the strong correlation between total oxalate-extractable Fe (Fe (oxal) ) and chromium-reducible sulfur (CRS = 0.2321 × total Fe (oxal) + 1.8180, r 2 = 0.3344, p = 0.0076) in the sediments suggested the rapid re-oxidation of sulfide and precipitation of sulfide with Fe. The turnover rate of the AVS at the H. nipponica bed (0.13 day −1 ) was 2.5 times lower than that at the Z. marina bed (0.33 day
−1). Together with lower AVS turnover, the stronger correlation of SRR to BGB in the H. nipponica bed suggests that the extension of H. nipponica resulting from the warming of seawater might provoke more sulfide accumulation in coastal sediments.