The effect of hot-water extraction and two types of fungal decay, brown rot and white rot, on wood crystalline cellulose structure was examined using a combination of X-ray diffraction (XRD) and 13C solid-state nuclear magnetic resonance (NMR) spectroscopy. Although having opposite effects on the overall crystallinity of the wood, the XRD results revealed that both extraction and brown-rot decay caused a significant decrease in the 200 crystal plane spacing (d-spacing) not seen for the white-rotted samples. This effect was found to be additive, as samples that were first extracted, then decayed showed a double decrease in d-spacing compared to that caused by extraction alone. This suggested that, despite having a similarly directed effect on the spacing of the crystalline planes, the two treatment methods facilitate a decrease in d-spacing in different ways. NMR results support the conclusion of differing structural effects, suggesting that the hot-water extraction procedure was causing a co-crystallization of existing crystalline domains, while the brown rot decay was depolymerizing the cellulose chains of the crystals, possibly allowing the remaining crystalline material the freedom to relax into a more energetically favorable, tightly packed state. These findings could have important implications for those seeking to understand the effects of modification treatments or biodegradation of crystalline cellulose nanostructures in their native states.