Waterlogged wood treatment with methyltrimethoxysilane (MTMS) proved effective in stabilising wood dimensions upon drying (anti-shrink efficiency of 76–93%). Before the method can be proposed as a reliable conservation treatment, further research is required that includes the evaluation of the mechanical properties of treated wood. The aim of the study was to characterise the effect of the treatment on the viscoelastic behaviour of archaeological waterlogged elm and oak wood differing in the degree of degradation. Dynamic mechanical analysis in the temperature range from −150 to +150 °C was used for the study. To better understand the viscoelastic behaviour of the treated wood, pore structure and moisture properties were also investigated using Scanning Electron Microscopy, nitrogen sorption, and Dynamic Vapour Sorption. The results clearly show that methyltrimethoxysilane not only prevents collapse and distortions of the degraded cell walls and decreases wood hygroscopicity (by more than half for highly degraded wood), but also reinforces the mechanical strength by increasing stiffness and resistance to deformation for heavily degraded wood (with an increase in storage modulus). However, the MTMS also has a plasticising effect on treated wood, as observed in the increased value of loss modulus and introduction of a new tan δ peak). On the one hand, methyltrimethoxysilane reduces wood hygroscopicity that reflects in lower wood moisture content, thus limiting the plasticising effect of water on wood polymers, but on the other hand, as a polymer itself, it contributes to the viscous behaviour of the treated wood. Interestingly, the effect of silane differs with both the wood species and the degree of wood degradation