<p dir="ltr">Density functional theory (DFT) is a widely used method to compute properties of materials, which are often collected in databases and serve as valuable starting points for further studies. In this article, we present the Materials Cloud Three-Dimensional Structure Database (MC3D), an online database of computed 3D inorganic crystal structures. Close to a million experimentally reported structures were imported from the COD, ICSD and MPDS databases; these were parsed and filtered to yield a collection of 72589 unique and stoichiometric structures, of which 95% are, to date, classified as experimentally known. The geometries of structures with up to 64 atoms were then optimized using DFT with automated workflows and curated input protocols. The procedure was repeated for different functionals (and computational protocols), with the latest version (MC3D PBEsol-v2) comprising 32013 unique structures. All versions of the MC3D are made available on the Materials Cloud portal, which provides a graphical interface to explore and download the data. The database includes the full provenance graph of all the calculations driven by the automated workflows, thus establishing full reproducibility of the results and more-than-FAIR procedures.</p> <p dir="ltr">This data entry includes the data with full provenance for all three versions: PBE-v1, PBEsol-v1 and PBEsol-v2.</p>