Musical instrument manufacturers have been led in recent years to reconsider the materials they use for instrument making, as shortages affect their wood supply. Materials such as plant fibre composites constitute a promising alternative, as they can reach similar properties to those of tonewood. The goal of this study is to provide a model-based method for comparing the vibration of guitars employing different materials for their soundboard, and to apply it to compare a flax fibre-based composite guitar soundboard to a spruce (Picea abies) reference. The instrument model, based on the finite element method and the Udwadia-Kalaba formulation, is used to synthesise transfer functions and plucked string signals. The effect of material substitutions on the guitar's sound characteristics are quantified by vibratory and audio descriptors. Similar trends are observed with both soundboard materials in terms of frequency response functions and some of the chosen audio descriptors.