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The design of optical devices is a complex and time-consuming process. To simplify this process, we present a novel framework of multi-fidelity multi-objective Bayesian optimization with warm starts, called Multi-BOWS. This approach automatically discovers new nanophotonic structures by managing multiple competing objectives and utilizing multi-fidelity evaluations during the design process. We employ our Multi-BOWS method to design an optical device specifically for transparent electromagnetic shielding, a challenge that demands balancing visible light transparency and effective protection against electromagnetic waves. Our approach leverages the understanding that simulations with a coarser mesh grid are faster, albeit less accurate than those using a denser mesh grid. Unlike the earlier multi-fidelity multi-objective method, Multi-BOWS begins with faster, less accurate evaluations, which we refer to as “warm-starting,” before shifting to a dense mesh grid to increase accuracy. As a result, Multi-BOWS demonstrates 3.2–89.9% larger normalized area under the Pareto frontier, which measures a balance between transparency and shielding effectiveness, than low-fidelity only and high-fidelity only techniques for the nanophotonic structures studied in this work. Moreover, our method outperforms an existing multi-fidelity method by obtaining 0.5–10.3% larger normalized area under the Pareto frontier for the structures of interest.