Optical nano multilayers (NMs) are promising candidates for durable transparent multifunctional coatings, although the contribution of interfaces and high transparency configurations has yet to be explored. To address this, high transparency NMs (%T380-1100nm≈94-99%) were synthesized by magnetron sputtering, and the effects of crystalline/amorphous (AlN/SiO2, AlN/Al2O3) and amorphous/amorphous (TiO2/SiO2) interfaces were characterized by spectrophotometry, transmission electron microscopy, and nanoindentation. We demonstrate that tuning layer configurations for improved transmittance resulted in substantial variations in microstructure and multifunctional film properties. Overall, this work presents a methodology for evaluating the structure-properties relationship in optical NMs in the context of interface character and layer microstructure.