This study aimed to examine the impact of Spartina alterniflora invasion and the replacement of Spartina alterniflora with Kandelia obovata (K.obovata restoration) on the abundance of soil ammonia-oxidizing microorganisms through real-time quantitative PCR analysis. Soil samples were collected from a native Cyperus malaccensis site, an area invaded by S.alterniflora, and a site undergoing K.obovata restoration in the Mingjiang River estuary, Fujian Province. The results revealed that significant impacts of both plant species and seasonal variations on soil physicochemical properties, wherein S.alterniflora invasion increased nitrate content, whereas K.obovata restoration decreased it. Soil pH, organic carbon, total nitrogen and ammonium nitrogen contents exhibited significant increases during winter compared to summer, while salinity demonstrated the opposite trend. Plant species had a significant impact on the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), with K.obovata restoration decreasing AOA abundance while increasing AOB abundance in winter. Although the influence of plant species on comammox Nitrospira was comparatively weaker, S.alterniflora invasion substantially reduced the abundance of comammox Nitrospiraclade A. Seasonal variations significantly influenced the abundance of AOB, which exhibited higher levels during winter compared to summer across all three plant species. In conclusion, K.obovata restoration led to a significant reduction in AOA abundance and an increase in AOB abundance during winter, along with a decrease in soil nitrate content, potentially influencing soil nitrification process.