This repository contains the dataset from the geometrical digital twinning of the as-built microstructure of three-leaf stone masonry walls of 700mm x 700 mm x 400 mm (Height x Length x Width) with laser scanning. It includes raw and processed data and data analysis scripts. A Readme file explains the structure of the dataset and the contents of each folder. The dataset corresponds to the journal paper Geometrical digital twins of the as-built microstructure of three-leaf stone masonry walls with laser scanning published on Scientific data https://doi.org/10.1038/s41597-023-02417-3. Please, cite as: Saloustros, S., Settimi, A., Ascencio, A.C., Gamerro, J, Weinand, Y., Beyer, K. Geometrical digital twins of the as-built microstructure of three-leaf stone masonry walls with laser scanning. Sci Data 10, 533 (2023). https://doi.org/10.1038/s41597-023-02417-3