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Soil salinity adversely limits crop and soil health, and this can be reversed by cropping systems where species exclude salts and activate microbial nutrient cycling. A randomized complete block design experiment was established in Laayoune-Morocco to evaluate the influence of irrigated grass pea and barley monocrops or combined together in 50-50% and 70-30% mixtures against soil salinity and CO 2 -C flux in sites with varying salinity. Site by treatment interaction significantly influenced (p < 0.05) soil salinity and CO 2 -C flux. Salinity reduced by 37 to 68 dS m -1 in highly saline soils across season regardless of treatment and barley monocrop retained the least salinity (15 dS m -1 ). Same applied to sites with low (1 to 2 dS m -1 ) and medium (2 to 5 dS m -1 ) salinity although less pronounced. The 70-30% grass pea, barley mixture maintained the greatest CO 2 -C flux in soils with low salinity and marginally enhancing soil active carbon (130 to 229 mg kg -1 soil) in different sites. Increasingly saline water filled pore space devastated CO 2 -C flux, although this process recovered under barley at extreme salinity. Overall, barley in mixture with grass pea can alleviate salinity and accelerate microbial carbon sequestration if irrigation is modulated in shallow desertic soils., (© 2023. Springer Nature Limited.)