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Global climate change and local anthropogenic activities are increasing soil salinization with permanent negative effects on agricultural and ecosystem productivity. While salt stress is known to affect plant performance, its effects on the association with key microbial plant symbionts, such as legume-associated nitrogen-fixing rhizobia, are less understood. In this field study conducted in Costa Rica (Puntarenas), we used sympatrically-occurring wild lima bean (Phaseolus lunatus L.) and Bradyrhizobium to quantify biomass production of unfertilized rhizobial (R+) and fertilized rhizobia-free (R-) plants at different levels of experimentally manipulated salinity in native soil. In response to salt stress, nodulation was significantly reduced even at slightly increased salt levels. Plants growing at soil salinity levels of 2, 4, 6, and 8 mS/cm showed a mean reduction of nodules by 60.22, 76.52, 83.98, and 92.5% compared to the controls. Similarly, we also observed a significant decline in plant biomass at elevated salinity. However, biomass accumulation of R- plants was significantly less impacted compared to R+ plants, suggesting that the plant-microbe symbiosis is more salt-sensitive than the plant host itself. We suggest that the search for more salt-tolerant, crop plant-compatible rhizobial strains may provide a sustainable approach to maintain agricultural productivity on low to moderately saline soils.