The goal of this study was to examine the impacts of sedimentary colonization by Suaeda heteroptera on benthic microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), 16S rRNA gene abundance, potential nitrification rate, and the richness and community structure of β-ammonia-oxidizing bacteria (β-AOB) in a salt marsh located in Shuangtai, China. Sediment samples (10-15 cm) were collected from a site colonized by S. heteroptera and from an adjacent unvegetated mudflat in July, August, September, and November of 2013. No significant differences in MBC were detected in unvegetated sediment among the various sampling dates, whereas MBC in vegetated sediment increased significantly in August and September compared with July (P ﹤ 0.05); overall, MBC in vegetated sediment was significantly higher than in unvegetated sediment (P ﹤ 0.05). A similar temporal trend was detected for MBN in the two sites, with higher values recorded in August than in July and November (P ﹤ 0.05); in addition, MBN in vegetated sediment increased significantly in July, August, and September compared with MBN in unvegetated sediment (P ﹤ 0.05). Bacterial 16S rRNA gene abundance, measured using a real-time quantitative PCR technique, was significantly higher in both habitats in July, August, and September than in November (P ﹤ 0.05), and was significantly higher in vegetated sediment in August, September, and November than in unvegetated sediment (P ﹤ 0.05). No significant differences in potential nitrification rates were detected within the two habitats for any of the sampling dates, but potential nitrification rate increased significantly in vegetated sediment in August and September compared with unvegetated sediment (P ﹤ 0.05). The abundance of β-AOB ammonia monooxygenase subunit A gene (amoA) in unvegetated sediment was significantly higher in August than in September and November (P ﹤ 0.05), but no difference was detected in the abundance of β-AOB amoA in vegetated sediment among the different sampling dates. However, β-AOB amoA abundance in vegetated sediment was significantly higher than in unvegetated sediment at all sampling dates (P ﹤ 0.05), with the exception of September. When data from all sampling dates were combined, MBN, 16S rRNA gene abundance, potential nitrification rate and abundance of β-AOB amoA were significantly higher in vegetated sediment than in unvegetated sediment (P ﹤ 0.05). The community structure of β-AOB was analyzed using the denaturing gradient gel electrophoresis (DGGE) technique. Sequences affiliated with species of Nitrosospira and Nitrosomonas were recovered from the two habitats. Colonization by S. heteroptera influenced the community structure and diversity of β-AOB. These results add to our understanding of the role microorganisms play in sediment dominated by S. heteroptera and provide a reference for the ecological restoration of salt marshes.