Autofluorescence generated by plant cells and tissues provides a label-free method for investigating them without altering their structure and biochemistry. While in the literature, research mainly focuses on investigating fresh plant tissues, this study examines flax yarns from five archaeological artefacts to understand how cell wall fibres degrade and how their biochemical composition is modified after natural ageing over millennia. Using Synchrotron-based deep UV fluorescence (S-DUV), we aim to correlate fibre autofluorescence with the environmental conditions of discovery (clothes of votive statuettes buried in a sanctuary or shrouds and bandages for mummification rituals found in tombs) or their intended purposes (fishing net, which underwent wet-dry cycles during its use). Out of the five archaeological objects studied, the two yarns sampled from the buried fabrics were found encrusted with minerals, but with significant differences in the fibres’ degradation. The yarn sampled from the fishing net displayed a great variability of the dataset, with some fibres biochemically similar to the buried samples while others were closer to the funerary linen shrouds. Lignin's predominant presence at 480 nm in the fishing net suggests extensive cellulose-enriched cell wall layer degradation while the lignin-enriched layer is still preserved. Additionally, second harmonic generation imaging microscopy (SHG) and 2-photon excitation fluorescence (2PEF) were used alongside S-DUV analyses to evaluate the flax fibres’ ultrastructure. SHG confirmed S-DUV findings and indicated poor crystalline cellulose preservation in one linen shroud, explaining the yarn's brittleness.