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Store Mosse (the ‘Great Bog’ in Swedish) is one of the most extensive bog complexes in southern Sweden (~77 km2), where pioneering palaeoenvironmental research has been carried out since the early 20th century. This includes, for example, vegetation changes, carbon and nitrogen dynamics, peat decomposition, atmospheric metal pollution, mineral dust deposition, dendrochronology, and tephrochronology. Even though organic matter (OM) represents the bulk of the peat mass and its compositional change has the potential to provide crucial ecological information on bog responses to environmental factors, peat OM molecular composition has not been addressed in detail. Here, a 568-cm-deep peat sequence was studied at high resolution, by attenuated reflectance Fourier-transform infrared spectroscopy (FTIR-ATR) in the mid-infrared region (4000–400 cm–1). Principal components analysis was performed on selected absorbances and change-point modelling was applied to the records to determine the timing of changes. Four components accounted for peat composition: (i) depletion/accumulation of labile (i.e. carbohydrates) and recalcitrant (i.e. lignin and other aromatics, aliphatics, organic acids and some N compounds) compounds, due to peat decomposition; (ii) variations in N compounds and carbohydrates; (iii) residual variation of lignin and organic acids; and (iv) residual variation of aliphatic structures. Peat decomposition showed two main patterns: a long-term trend highly correlated to peat age (r = 0.87), and a short-term trend, which showed five main phases of increased decomposition (at ~8.4–8.1, ~7.0–5.6, ~3.5–3.1, ~2.7–2.1 and ~1.6–1.3 ka) – mostly corresponding to drier climate and its effect on bog hydrology. The high peat accumulation event (~5.6–3.9 ka), described in earlier studies, is characterized by the lowest degree of peat decomposition of the whole record. Given that FTIR-ATR is a quick, non-destructive, cost-effective technique, our results indicate that it can be applied in a systematic way (including multicore studies) to peat research and provide relevant information on the evolution of peatlands.