This article contains data related to the research article entitled "An Investigation of Organic Matter Quality and Quantity in Acid Soils as Influenced by Soil Type and Land Use" (Shen et al., 2018) [1]. The data was collected using a chemical fractionation scheme of soil organic matter (OM). This involved the separation of organic carbon (OC) fractions based on their solubility in (i) cold and hot water, (ii) 0.1 M sodium pyrophosphate (pH ~ 10), and (iii) 2% HF solution, and the residue remaining after the HF extraction. The OM in this residue, after treatment with 2% HF solution, was characterised using pyrolysis (Py)-GC/MS. This technique involves thermal decomposition of OM into various pyrolysis products, which are then chromatographically separated and determined by mass spectroscopy. This technique has been used to semi-quantify individual soil OM constituents so that in-depth information on soil OM molecular fingerprints is provided. This article presents a detailed dataset of physical-chemical characterization, OC fractions and OM molecular fingerprints of 62 soil samples for a range of soil orders (i.e., Allophanic, Brown, Gley, Pallic and Recent) and land uses (i.e., permanently grazed pasture, ungrazed/unmanaged grasslands, annual cropping) across New Zealand. Principal component analysis was used to investigate the relationships of different soil properties with OC fractions and OM chemistry so that the underlying mechanisms responsible for the differences encountered in OM quantity and quality between soil orders and land uses are understood.