Land application of organic waste is an important alternative to landfilling and incineration because it helps restore soil fertility and has environmental and agronomic benefits. These benefits may be related to the biochemical composition of the waste, which can result in the accumulation of different types of carbon compounds in soil. The objective of this study was to identify and characterise changes in soil organic matter (SOM) composition after repeated applications of organic waste. Soil from the CRUCIAL field experiment in Denmark was sampled after 12 years of annual application of household waste compost, cattle manure and sewage sludge, and was compared to a control treatment that had received NPK fertilisation. Soils were characterised using CO₂-evolved gas analysis (CO₂-EGA) during ramped thermal analysis, mid-infrared photoacoustic spectroscopy (FTIR-PAS) and analysis of amino-sugar and lignin phenols. SOM from the compost and cattle manure treatments had greater thermal stability than the sludge and NPK treatments, which was consistent with the thermal stability of the applied wastes. Compost-amended soils and manure-amended soils also had a greater lignin content with a lower degree of oxidation and a greater contribution of bacterial amino sugars relative to fungal amino sugars compared to soils from the NPK treatment. The high soil C accumulation rate combined with low amino sugar C in SOM from the compost treatment suggested less stimulation of microbial activity, while the cattle manure seemed to result in both microbial stimulation and accumulation of thermally stable forms of C. FTIR-PAS revealed greater C=O vibration of carboxylic groups and amides in sludge and NPK treatments, indicating more oxidised SOM and the presence of proteins. Taken together, these results show that there was accumulation in soil of different C compounds for the different types of applied organic waste, which appeared to be related to the degree to which microbial activity was stimulated and the type of microbial communities applied with the wastes or associated with the decomposition of applied wastes. This in turn may have important effects on ecosystem functioning and long-term soil C storage.