Global climate change and human interference gradually increase the salt-affected land; hence the availability of agricultural land is decreasing day by day. Higher salinity severely affects the physical, chemical and biological characteristics of the soil. Various studies investigated the effects of growing crop plants on soil quality but such investigations on halophytic plants in their natural habitat are limited. Salicornia brachiata was selected to assess its effects on the soil quality over temporal and spatial scales because of its highest importance value index among the naturally growing coastal halophytes at the studied sites. The root zone soil of S. brachiata was sampled (six times in one growing period) from six different coastal sites in Gujarat, India. Soil characteristics, microbial community composition (ester linked-fatty acid methyl ester profiling) and genes (16S rRNA, nifH and cbbL) abundance in comparison with control soil (without vegetation) were studied. The root zone soil of S. brachiata had significantly higher pH, K+ and P, and lower EC, NO3–-N, NH4+-N and Na+ contents than control soil. The contents of total, GM+ve, GM−ve, total bacterial, fungal and actinomycetes FAMEs (fatty acid methyl esters) were higher in the S. brachiata covered soils (37.98, 6.44, 10.38, 16.35, 1.74 and 2.12 nmol g−1, respectively) than control soils (22.22, 3.81, 5.47, 9.30, 0.77 and 1.23 nmol g−1, respectively). Among the studied sites, root zone soil from Diu possessed the highest total, bacterial (GM+ve and GM−ve), fungal and actinomycetes FAMEs, whereas the Vivaniya site exhibited the lowest. Among the sampling periods, S. brachiata soil exhibited significantly elevated contents of total FAME and FAME biomarkers of microbial taxonomic groups in the initial two sampling months (August and October), followed by December and the least in June. Compared with control soil, S. brachiata covered soil possessed the microbial community shift related to the enhanced abundance of total bacterial, GM−ve and fungal FAMEs. The abundance of 16S rRNA, cbbL and nifH genes was higher in S. brachiata covered soils (1.64 × 109, 5.06 × 106 and 2.53 × 107, respectively) compared with control soil (6.78 × 108, 1.55 × 106 and 6.99 × 106, respectively). In the August and October months, the abundance of all three genes was highest in S. brachiata and control soils. The findings of this study confirm the significant effects of S. brachiata on saline soil properties (soil characteristics, microbial activities and genes abundance) over temporal and spatial scales. The results strongly suggest the potentials of S. brachiata for the restoration of salt-affected degraded lands for healthy ecosystem functioning.