The microstructures of building materials from the archaeological complex of Huaca de la Luna on the northern coast of Peru is assessed for the first time by a multiscale approach. The multiscale microstructural characterization used laboratory techniques including optical microscopy, scanning electron microscopy, X-ray microtomography, and both gas and powder pycnometry. Optical microscopy revealed the presence of organic matter and shell fragments and X-ray microtomography showed differences in the sizes and connectivity of pores. The BET (N2 gas adsorption) specific surface areas showed greater presence of clayey matrix in the mortars. No significant differences among mortars and brick fragments mineralogy were detected by X-ray diffraction, so the larger amount of fine binding matrix in the mortars suggests that they were produced blending raw material with different grain sizes. The aim of this study is to provide data that can be used for a better understanding of the Moche culture, its construction techniques, and to support conservation strategies of the archaeological heritage.