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Understanding the impacts of tillage on soil microflora, especially functional microbes related to nitrogen conversion, is essential for ensuring the sustainable production, biodiversity and function of agroecosystems in salinized soils. Based on a two-year field plot experiment in a salt-affected farmland, the effects of three tillage methods, namely, CT (conventional rotary tillage, depth 25 cm), VRT (vertical rotary tillage, depth 25 cm) and DVRT (deep vertical rotary tillage, depth 50 cm), on soil physicochemical properties and ammonia-oxidizing archaea (AOA), bacteria (AOB) and comammox bacteria (CAOB) communities were investigated. Soil samples over the sunflower (Helianthus annuus L.) growing season were collected on three dates, i.e., April 28, July 6, and September 6, 2020. The results indicated that CT, VRT and DVRT had the lowest EC 1:5 values (0.75–1.23 dS/m) and the highest OC (organic carbon, 14.50–19.32 g/kg), WSA1 (> 2 mm water-stable aggregates, 31.05–37.88 g/kg), and WSA2 (2–0.25 mm water-stable aggregates, 69.51–83.70 g/kg) values on the middle sampling date. The average number of OTUs was 51.2 ± 3.3, 43.2 ± 3.8 and 42.8 ± 6.2 (mean ± SD) per soil sample for AOA, AOB and CAOB, respectively. DVRT significantly affected the community richness indices (Sobs, ACE and Chao1) of AOA and AOB, whereas sampling dates shifted almost all the soil physicochemical properties and diversity indices (Shannon and Simpson) of AOA and AOB but not those of CAOB. Phyla Crenarchaeota , unclassified_d_Unclassified , Unclassified_k_norank_d_Archaea and Thaumarchaeota were the most common taxa (with relative abundances >5 %) of AOA under all the treatments. For AOB, >92 % of the taxa were categorized into the phylum Proteobacteria , and CT had a greater frequency of the phylum Proteobacteria than did VRT and DVRT on all sampling dates. For CAOB, approximately 90 % of the taxa were classified into the phylum Nitrospirae , and the relative abundance of Nitrospirae did not differ among the tillage practices, whereas VRT and DVRT had the highest relative abundance of Nitrospirae on the middle sampling date. A total of 88.69 % of the variation in the genus compositions of AOA, AOB and CAOB was explained by EC 1:5 , pH, OC, ρ b (bulk density), WSA1 and WSA2. In conclusion, tillage practices and sampling dates can diversely affect soil physicochemical properties, microbial richness and diversity indices of AOA, AOB and CAOB, and seasonal changes overwhelm tillage practices in shaping AOA, AOB and CAOB communities across the sunflower growing season in salinized irrigated farmland. • Tillage and sampling date dominated richness and diversity, respectively, for AOA and AOB. • Community richness and diversity of CAOB were only responsive to sampling date. • Tillage and seasons affected microbial communities by changing EC 1:5 , pH, OC, ρ b , WSA1 and WSA2. • Seasons overwhelmed tillage in shaping AOA, AOB and CAOB communities in sunflower growing season. [ABSTRACT FROM AUTHOR]