A numerical model is developed and validated to analyse the performance of aluminium skin and agglomerated cork core sandwich plates subjected to blast loads. Two numerical approaches are used and thoroughly compared to generate the blast loading: an Arbitrary-Lagrangian–Eulerian approach and the Load Blast Enhanced method. Both of the models are validated by comparing the numerical results with experimental observations. A detailed analysis of the sandwich behaviour is done for both approaches showing small differences regarding the mechanical response of the sandwich structure. The results obtained from the numerical models uncover the specific energy absorption mechanisms happening within the sandwich plate components. A new core topology is proposed, based on these results, which maximises the energy absorption capacity of the plate, keeping the areal density unchanged. A wavy agglomerated cork core is proposed and the effects of different geometrical parameters on the energy absorption are thoroughly analysed and discussed. The proposed optimised plate configuration shows an increase in the total absorbed energy of close to 40% relative to a reference case with the same areal density. The adopted optimisation methodology can be applied to alternative configurations to increase the performance of sandwich structures under blast events.