The mechanical properties of Opalinus Clay shale are strongly affected by the mineralogical composition of the layers and by their spatial arrangement at centimetre to decimetre scales. For this reason, accurate laboratory characterization of the mechanical properties, in many cases, is not representative of the material behaviour at a larger scale. A new approach is proposed to integrate petrophysical information from boreholes with small-scale mechanical laboratory characterization to extrapolate the distribution of mechanical properties to the scale of the engineering problem. The workflow is based on two fundamental concepts: defining a layering setting at different length scales from petrophysical investigations and creating a numerical representation of the mineralogically homogeneous layers. Merging the two concepts, it is possible to define the layered geometry of a finite element analysis of the laboratory tests used to calibrate the mechanical properties of the homogeneous layers. Once the properties of the layers have been assessed, the upscaling process can be performed using the geometric configuration at larger length scales. The layering setting is deduced, at the core scale, from petrophysical measurements and then extended by geostatistical prediction to the borehole scale. The workflow has been applied in a series of high accuracy laboratory tests to obtain the spatial distribution of mechanical properties at the borehole scale on the basis of the layering configuration deduced from a series of X-ray computed tomography tests.