During long-term laboratory incubations, declining soil-breathing rates are reliably observed. The explanation for this decrease is unclear, however. We analyzed various ground breathing controls to explain drivers of increased breathing rate during organic matter incubations in calcareous soil and lower breathing rate in saline soil. The soil was substantially depleted from soil carbon and microbial biomass following long-term incubators of soils from two sites (saline-sodic and calcareous soils at Northwestern, Alexandria, Egypt). We have exposed soils to 150 days incubation with nine treatments included two levels of spent grain (beer industry organic wastes) was referred to as 10 g kg–1 soil (S1), and 20 g kg–1soil (S2); two levels of compost were referred to as 10 g kg–1 soil (M1), and 20 g kg–1 (M2); inoculation of Azospirillumbrasilense (A1) (one of the plant growth-promoting rhizobacteria), was inoculated 5% weight of the soil; a mix of both sources M1 and S1 (M1S1); a mix of both sources A1with M1 and S1 (A1M1) and (A1S1); all treatments were used and compared to the control without amendments. All treatments were mixed with soil samples (400 g) placed in 500 ml un-covered glass bottles placed within the sealed incubator. These treatments were arranged in a randomized complete block design and replicated three times. Results showed that the soil respiration was consistently higher (2-1.2 times) higher in calcareous soil than saline-sodic soil. The average soil cumulative CO2 emission values for both soils showed the most elevated S2 and A1 treatments 548.3 and 364 mg C 100 g–1 soil. The lowest was observed for the control treatment 89.12 and 40.13 mg C 100 g–1 for calcareous and saline soils, respectively. Simultaneously, M2 and S1 treatments had similar soil respiration values at 150 days of soil incubation, respectively. Further, the microbial biomass levels were more exchanged in soils degraded by incubation after 90 days of calcareous soil incubation. The levels of microbial biomass in soils were very small in the saline compared with calcareous soil. In incubation soils, 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 highest values of the dehydrogenase and urease enzymes in calcareous soil, 720 μg TPF ml–1, and 309 mg NH3 Hg–1h–1), respectively after 150 days of soil incubation. On the other hand, the A1S1 and A1 treatments were the more significant in dehydrogenase and urease enzymes in saline-sodic soil was 238.3 μg TPF ml–1, and 603 mg NH3 Hg–1 h–1, respectively after 150 days of soil incubation. In conclusion, our findings support the idea that the soil organic matter additives increased soil respiration over long-term incubations instead of the absence of microbial biomass and enzymes in calcareous more than saline soils. Due to significant soil biomass change during extensive incubation, this decomposition of both bio and organic additives changed the inability to quantify the soil biomass in both calcareous and saline soils.