In this paper, a Floquet Model Order Reduction (MOR) method is proposed for the modelling of finite periodic structures subjected to harmonic or transient loads. This Floquet MOR generates frequency-independent projection matrices of the full-scale structure using a Floquet expansion of the local state-vectors computed on a single unit-cell with the Forced Wave Finite Element framework. This two-step MOR method can handle large multi-scale waveguides regardless of the scale and the number of unit-cells. A comparison with a standard sub-structuring approach based on unit-cell wave-mode reduction demonstrates that Floquet MOR is able to create reduced models of finite periodic structures with an unequalled computational efficiency. The method’s ability to produce small and accurate models suitable for time-domain simulations presents a high potential for virtual sensing, real-time Structural Health Monitoring (SHM) and digital twins for large periodic structures and metamaterials.