Soil organic carbon (SOC) storage can be increased by incorporating crop residues such as straw. However, the use of straw as a bioenergy source is an alternative option. There is currently great uncertainty concerning the effects of residue incorporation/removal, but estimates can be improved by using well-documented, frequently sampled long-term experiments (LTEs). This study examined the effect of straw incorporation on SOC stocks in six Swedish LTEs (duration of 27–56 years), using data from 5 to 28 sampling occasions. A total of 16 pairs of straw incorporation (SI) and straw removal (SR) treatments were compared and modelled with the ICBM/2 model (two young pools with distinct humification coefficients, h), which enabled us to clearly isolate the effect of straw carbon input. The model results were compared to the Ultuna frame trial, as the first and only parameterization site of ICBM. At five out of six sites, the humification coefficient for straw (hlitter) was much smaller (0–0.09) than the ICBM default h value for plant material (0.125). The derived hlitter values and thus the stabilization of straw derived carbon increased significantly with clay content. An Italian site with five pairs of SI and SR treatments was used to test the performance of ICBM/2 under contrasting pedoclimatic conditions. Similar to the Swedish sites, the best model fits were found with hlitter values ranging from 0 to 0.05 increasing with nitrogen fertilization (range of 0–240 kg N ha− 1 yr− 1), which was attributed to changes in substrate use efficiency of microbes. However, this trend was not consistent for all sites. For future applications of ICBM/2, we suggest using the validated clay function to derive hlitter for common levels of nitrogen fertilization. The efficiency of incorporating straw to increase SOC stocks depends on soil texture and using it for bioenergy production could be a more sustainable and climate-smart option.