Cross-border geological models provide a useful basis for the development of shared understanding of the underground/subsurface and thus assisting the promotion and diffusion of geological data across neighbouring nations and the management of transborder natural resources (i.e. underground water, geothermal fluids, hydrocarbons, etc.) and possible associated issues (ground water pollution and over exploitation, etc.). Effective engineering of cross-border projects, such as underground infrastructures or regional groundwater protection programs, relies on a solid and uniform geodatabase system. In the case of the Canton of Geneva in Switzerland and neighbouring France, the geological knowledge of the subsurface is inconsistent. More specifically, data type, coordinate reference system, well stratigraphy description, etc., are organised and structured in a very different database architecture. In this study, we collected, integrated, harmonised and stored geological data from the BRGM’s InfoTerre subsurface database (French geological survey), into U_SOLSTISS, a Unige local version of the official SOLSTISS database (New subsurface information system of the Canton of Geneva) developed by GESDEC (Geology, Soils and Waste Department of the Canton of Geneva). This study focuses on the Quaternary strata in order to harmonise the well stratigraphy of cross-border areas, addressing the occurrence, extension and distribution of different glacial and interglacial cycles across the Geneva Basin and neighbouring France. This study, therefore, presents a homogenous and harmonised cross-border Quaternary stratigraphic scheme database that highlights the lateral and vertical characteristics of the geological units in the study area. This ultimately serves as crucial input necessary for providing an updated Model of the Base Quaternary/ Top Molasse surface, which will be used in the framework of the feasibility project for the new CERN Future Circular Collider (FCC), a new research facility tunnel located at a depth of ca. 200 m with a circumference of 90.7 km.