This paper describes the synthesis and characterization of macro-mesoporous ZnO inverse opals through a template-based approach. In addition, the distribution and diffusion of a fluorescent organic tracer molecule (Alexa Fluor 488) through quasi-mesoporous ZnO inverse opals was investigated via confocal laser scanning microscopy (CLSM) and fluorescence correlation spectroscopy (FCS). The attached data consists of relevant scanning electron microscope (SEM) images, particle and pore-size distributions, film thickness data, X-ray diffraction (XRD) patterns, ultraviolet-visible (UV-Vis) spectra, CLSM images and FCS spectra. The following data formats are used: tif, .png, .xlsx and .xy. The data files are ordered as per their appearance in the publication.