Soil organic matter (SOM) is composed of fractions with different functionsand reactivity. Among these, particulate organic matter (POM) is the maineduct of new inputs of organic matter in soils and its chemical fate correspondsto the first stages of the SOM decomposition cascade ultimately leading to theassociation of organic and mineral phases. We aimed at investigating themolecular changes of POM during decomposition at a sub-millimetre scale bycombining direct measurements of POM elemental and molecular compositionwith laboratory imaging visible–near-infrared (VNIR) spectroscopy. For this,we set up an incubation experiment to compare the molecular composition ofstraw and composted green manure, materials greatly differing in their C/Nratio, during their decomposition in reconstituted topsoil or subsoil of a Luvisol,and recorded hyperspectral images at high spatial and spectral resolutions ofcomplete soil cores at the start and end of the incubation. Hyperspectral imagingwas successfully combined with machine learning ensembles to produce a pre-cise mapping of POM alkyl/O-N alkyl ratio and C/N, revealing the spatial het-erogeneity in the composition of both straw and green manure. We found thatboth types of organic amendment were more degraded in the reconstituted top-soil than in subsoil after the incubation. We also measured consistent trends inmolecular changes undergone by straw, with the alkyl/O-N alkyl ratio slightlyincreasing from 0.06 to 0.07, and C/N dropping by about 40 units. The greenmanure material was very heterogeneous, with no clear molecular changesdetected as a result of incubation. The imaging VNIR spectroscopy approachpresented here enables high-resolution mapping of the spatial distribution of themolecular characteristics of organic particles in soil cores, and offers opportuni-ties to disentangle the roles of POM chemistry and morphology during the firststeps of the decomposition cascade of organic matter in soils.