Wood decay is an economically significant process, as it is one of the major causes of wood deterioration in buildings. In this study, the decay process of Scots pine (Pinus sylvestris) samples caused by cellar fungus (Coniophora puteana) was followed by nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) methods. Altogether, 30 wood sample pieces were exposed to fungus for 10 weeks. Based on the decrease of the dry mass, the samples were categorized into three classes: decomposed (mass decrease 50–70%), slightly decomposed (10–50%), and nondecomposed (<10%). MRI made it possible to identify the active regions of fungus inside the wood samples based on the signal of free water brought by the fungus and arisen from the decomposition of wood carbohydrates. MRI implies that free water is not only created by the decay process, but fungal hyphae also transports a significant amount of water into the sample. Two-dimensional 1H T1-T2 relaxation correlation NMR measurements provided detailed information about the changes in the microstructure of wood due to fungal decomposition. Overall, this study paves the way for noninvasive NMR and MRI detection of fungal decay at early stages as well as the related structural changes.