The application of organic amendments is an important technique used to enhance carbon storage in soils, thereby reducing CO2 emissions and mitigating climate change. The role of the composition of organic amendment in CO2 emissions is not well understood, however. The aim of this study was to understand the effect of the biochemical composition of organic amendments on CO2 emission and carbon stabilization. To do this, the application to the soil of five organic amendments with different biochemical compositions was considered. The effects of two types of compost (CH and CP), green manure (GM), olive mill waste water (OMW) and manure (M) on the rate of mineralization and humification of organic carbon were studied under controlled conditions. A single dose of 350 mg of organic carbon/100 g of soil was tested. These treatments, and the control soil, were incubated for 56 days. Soil respiration, organic carbon evolution, and the polymerization index were measured during the incubation period. The results showed that CO2 emission was strongly associated with the soluble fraction and the lignin content. Olive mill water, with the highest soluble fraction, induced the highest rate of mineralization. Composts CH and CP, with the greatest lignin content, were the most resistant to short‐term decomposition, and permitted the highest amount of carbon to be stored in the soil. Overall, this study showed that composts were the best form of organic C application. Indeed, with the composts, low direct mineralization was detected, improving the humidification processes and resulting in enhanced C storage in the soil. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd.