PLA-flax non-woven composites are promising materials, coupling high performance and possible degradation at their end of life. To explore their ageing mechanisms during garden composting, microstructural investigations were carried out through scanning electron microscopy (SEM) and atomic force microscopy (AFM). We observe that flax fibres preferentially degrade ‘inwards’ from the edge to the core of the composite. In addition, progressive erosion of the cell walls occurs within the fibres themselves, ‘outwards’ from the central lumen to the periphery primary wall. This preferential degradation is reflected in the decrease in indentation modulus from around 23 GPa for fibres located in the preserved core of the composite to 3–4 GPa for the remaining outer-most cell wall crowns located at the edge of the sample that is in contact with the compost. Ageing of the PLA matrix is less drastic with a relatively stable indentation modulus. Nevertheless, a change in the PLA morphology, a significant decrease in its roughness and increase of porosity, can be observed towards the edge of the sample, in comparison to the core. This work highlights the important role of intrinsic fibre porosity, called lumen, which is suspected to be a major variable of the compost ageing process, providing pathways of entry for moisture and microorganisms that are involved in cell wall degradation.