This data article describes the detailed parameters for synthesizing mullite inverse opal photonic crystals via Atomic Layer Deposition (ALD), as well as the detailed image analysis routine used to interpret the data obtained by the measurement of such photonic crystals, before and after the heat treatment, via Ptychographic X-ray Computed Tomography (PXCT). The data presented in this article are related to the research article by Furlan and co-authors entitled “Photonic materials for high-temperature applications: Synthesis and characterization by X-ray ptychographic tomography” (Furlan et al., 2018). The data include detailed information about the ALD super-cycle process to generate the ternary oxides inside a photonic crystal template, the raw data from supporting characterization techniques, as well as the full dataset obtained from PXCT. All the data herein described is publicly available in a Mendeley Data archive "Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals" located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes.