Soil carbon and microbial biomass were substantially depleted following long-term incubation for saline-sodic and calcareous soils. The objectives of the present study were to investigate changes in (i) soil CO₂-emissions and (ii) soil fertility and SOM decomposition (iii) soil enzymes activities during the incubation period under various organic and biological soil treatments. Both soils were incubated for 150 days with 9 treatments included 2 levels of spent grain, which referred to as 10 g kg⁻¹ soil (S1), and 20 g kg⁻¹ soil (S2); two levels of compost were referred to as 10 g kg⁻¹ soil (M1), and 20 gkg⁻¹(M2); Azospirillum brasilense (A1) was inoculated 5% of weight of the soil; the mix of both sources M1 and S1 (M1S1); the combination of both sources A1 with M1 and S1 (A1M1) and (A1S1); all treatments were used and compared to the control. All treatments were mixed with 400 g soil samples and incubated at 28°C. Results showed that the average cumulative CO₂ emission for both soils regarding to S2 and A1 treatments had the highest values, 548.3 and 364 (mg C100g⁻¹ soil), respectively. While the lowest value was observed for the control treatment 89.12 and 40.13 (mg C100g⁻¹ soil) for calcareous and saline soils, respectively. The dehydrogenase and urease enzymes were often decreased slightly and did not respond to adding labile substrate, and did not restrict soil breathing. The S2 treatment possessed the dehydrogenase and urease enzymes highest values in calcareous soil, 720 (μgTPFml⁻¹) and 309 (mgNH₃⁻Hg⁻¹h⁻¹), respectively, after incubation periods. In conclusion, the findings support the idea that the soil organic matter amendments increased soil respiration over long-term incubation and compensate the absence of microbial biomass and enzymes in calcareous more than saline soils and enhance soil-plant nitration.