Plants have evolved a wide range of adaptation mechanisms that enable them to grow and develop in environments of high soil salinity. We examine the plant—microbial interactions of Salicornia europaea (Herbaceae) as potential mechanisms responsible for the high tolerance of halophytes to saline conditions. We evaluated the impact of different NaCl concentrations on microorganisms associated with S. europaea growing at 2 saline sites in central Poland: a salty meadow in the vicinity of a soda factory (anthropogenic salinity) and an area affected by natural brine (landscape park). The community-level physiological profiles of microorganisms associated with the plant were determined for endophytes from the roots, rhizosphere, and salt-affected soil. The highest total microbial metabolic activity, irrespective of the test site, was always in the rhizosphere, while the activity of endophytic and soil populations depended on salinity. In general, a higher total metabolic activity was observed at the test site exhibiting higher salt concentration. We propose that increased metabolic activity of microbial populations under increased salt stress can significantly contribute to the site adaptation of halophytes to saline conditions.