This paper investigates the seismic protection of the Nuward™ small modular reactor (SMR) building, focusing on design loading and beyond design basis earthquake (bDBE) conditions. The study aims to achieve two primary objectives: i) to enhance seismic mitigation of a SMR building under bDBE conditions, through the use of the innovative modular single-layer (SLM) and multi-layer (MLM) metafoundations (MFs); ii) to effectively standardise and harmonise SMR building designs in locations prone to beyond design basis conditions. To accomplish these goals and demonstrate the protective capabilities of the MFs, the study employs non-linear time-history analyses (NLTHAs) for both DBE and bDBE conditions. Along these lines, a reduced-order model was developed from a refined finite element (FE) model of the SMR building using the Craig-Bampton mode synthesis technique. Then, finite locally resonant modular MFs were designed and analysed using NLTHAs. Specifically, physics-based ground motion models (GMMs) were used to generate and select seismic triplets that mimicked DBE and bDBE scenarios for NLTHAs. Successively to achieve improved seismic performance, the optimization of the MFs was pursued by targeting the optimal number of columns, resonator parameters, and unit cell dimensions. Additionally, the deployment of inerters was considered, to significantly reduce the size of the MFs and enable their application in multiple layers for ultra-low frequency attenuation. The overall findings suggest that modular MFs meet seismic protection requirements, and positively contribute to the standardization process of SMR buildings, even in areas characterized by beyond-design seismic conditions.