Near infrared (NIR) and mid-infrared (mid-IR) reflectance spectroscopy are time- and cost-effective tools for characterising soil organic carbon (SOC). Here they were used for quantifying (i) carbon (C) dioxide (CO2) emission from soil samples crushed to 2 mm and 0.2 mm, at 18°C and 28°C; (ii) physical C protection, calculated as the difference between CO2 emissions from 0.2 mm and 2 mm crushed soil at a given temperature; and (iii) the temperature vulnerability of this protection, calculated as the difference between C protection at 18°C and 28°C. This was done for 97 topsoil samples from Tunisia, mostly calcareous, which were incubated for 21 days. Soil CO2 emission increased with temperature and fine crushing. However, C protection in 0.2–2 mm aggregates had little effect on the temperature vulnerability of CO2 emission, possibly due to preferential SOC protection in smaller aggregates. In general, NIR spectroscopy, and to a lesser extent mid-IR spectroscopy, yielded accurate predictions of soil CO2 emission (0.60 ≤ R² ≤ 0.91), and acceptable predictions of C protection at the beginning of incubation (0.52 ≤ R² ≤ 0.81) but not over the whole 21 day period (R² ≤ 0.59). For CO2 emission, prediction error was the same order of magnitude as, and sometimes similar to, the uncertainty of conventional determination, indicating that a noticeable proportion of the former could be attributed to the latter. The temperature vulnerability of C protection could not be modelled correctly (R² ≤ 0.11), due to error propagation. The prediction of SOC was better with NIR spectroscopy and that of soil inorganic C (SIC) was very accurate (R² ≥ 0.94), especially with mid-IR spectroscopy. Soil CO2 emission, C protection and its vulnerability were best predicted with NIR spectra, those of 0.2 mm samples especially. With 2 mm samples, mid-IR spectroscopy yielded the worst predictions in general. NIR spectroscopy prediction models suggested that CO2 emission and C protection depended (i) on aliphatic compounds (i.e. labile substrates), dominantly at 18°C; (ii) on amides or proteins (i.e. microbial biomass), markedly at 28°C; and (iii) negatively, on organohalogens and aromatic amines (i.e. pesticides). Models using mid-IR spectra showed a negative influence of carbonates on CO2 emission, suggesting they did not contribute to soil CO2 emission and might form during incubation. They also suggested that CO2 emission and C protection related to carboxylic acids, saturated aliphatic ones especially.