With increasing awareness of the ecological value of trees in urban areas, there is a growing need to preserve mature specimens often colonised by wood-decay fungi. Nonetheless, cases of stem collapse or uprooting of such trees under adverse weather conditions remain a significant issue requiring further investigation. Depending on the decay type and the wood structure of the host tree, different combinations of wood-decaying fungi and host species can have varying impacts on the mechanical and vibroacoustic properties of green wood. This study compares the physical and mechanical properties of green European beech (Fagus sylvatica L.) and small-leaved linden (Tilia cordata Mill.) artificially exposed to Fomes fomentarius (L.) Fr. and Kretzschmaria deusta (Hoff.) P.M.D. Martin after different exposure periods. Mass loss (ML) caused by both fungi differed according to the wood species. A statistically significant difference between the two fungal species was observed in beech wood, but not in linden. Significant differences in the modulus of rupture (MOR) and dynamic bending modulus of elasticity (MOED) were observed among the fungus-wood combinations, also depending on the exposure time. The relationships between ML and MOR varied according to the fungal species, where at the same ML values, K. deusta caused a higher MOR loss in both wood species. Strong relationships between MOED and MOR were demonstrated for all fungus-wood combinations, without significant differences related to the decay type. The MOED is a reliable parameter for predicting MOR loss even at incipient degradation stages, irrespective of the type of decay. The presented results can lead to better prediction of the impact of fungal colonization on standing trees and improve non-destructive methods used for tree stability assessment.