In the present work, a physically-based finite element model simulating the compression moulding process of cork-based agglomerates is presented. The goal is the prediction of the pre-stress state due to the process and its influence on the macroscopic mechanical properties of the agglomerate. An ad-hoc algorithm simulating the mould filling phase (based on a generalised Voronoi's tesselation algorithm which is paired with a 2D physics engine) as well as the moulding compression phase is presented. A numerical campaign is conducted to show the effectiveness of the modelling strategy and to assess the influence of packing density on the behaviour of the agglomerate. For all considered cases, the stress-strain and time dependent density curves of the agglomerate show that a high packing density configuration, resulting from a proper selection of particles size mixing, allows obtaining higher tangent moduli than that of natural cork with a lower material density.