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Polymer nanodielectrics present a particularly challenging materials design problem for capacitive energy storage applications like polymer film capacitors. High permittivity and breakdown strength are needed to achieve high energy density and loss must be low. Strategies that increase permittivity tend to decrease the breakdown strength and increase loss. We hypothesize that a parameter space exists for fillers of modest aspect ratio functionalized with charge-trapping molecules that results in an increase in permittivity and breakdown strength simultaneously, while limiting increases in loss. In this work, we explore this parameter space, using physics-based, multiscale 3D dielectric property simulations, mixed-variable machine learning and Bayesian optimization to identify the compositions and morphologies which lead to the optimization of these competing properties. We employ first principle-based calculations for interface trap densities which are further used in breakdown strength calculations. For permittivity and loss calculations, we use continuum scale modelling and finite difference solution of Poisson’s equation for steady-state currents. We propose a design framework for optimizing multiple properties by tuning design variables including the microstructure and interface properties. Finally, we employ mixed-variable global sensitivity analysis to understand the complex interplay between four continuous microstructural and two categorical interface choices to extract further physical knowledge on the design of nanodielectrics.