As a natural material, wood is susceptible to degradation processes, preserving equilibrium between buildup and breakdown of biomass. Microorganisms, such as fungi or bacteria, play a major role in the degradation processes in wood. Their activity depends on the environmental conditions: in ambient conditions fungal degradation is dominant while in waterlogged conditions mainly bacterial degradation occurs. Wood exhibits a hierarchical organization. Thus, mechanical properties of a piece of solid wood depend on its inherent heterogeneous microstructure. Starting from the annual rings, individual wood cells and their cell wall layers can be identified as hierarchical levels. The so-called S2 cell wall layer and the middle lamella between individual wood cells dominate the macroscopic behaviour of wood. Thus the properties of these two layers are of particular interest. Their mechanical properties can be assessed by means of nanoindentation. During nanoindentation, a probe is pushed into a flat sample surface and from the subsequent unloading behavior, material properties, such as the indentation modulus and the indentation hardness, can be determined. In contrast to findings at the macroscopic scale, no stiffness losses were detected in degraded cell wall layers. Even slightly increased stiffness of the S2 layer and the middle lamella were measured in material degraded either by fungi or bacteria. Concurrently, microstructural and chemical analyses of the degraded material were conducted. Both multivariate data analysis as well as micromechanical modeling enables establishing structure-function relationships also for degraded wood cell walls.