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Summary Determining the elastic properties of organic-rich shales through traditional geomechanical testing is often challenging due to the pronounced heterogeneity of shale specimens and the limited availability of high-quality core plugs. In this context, nanoindentation has emerged as an effective technique for probing the elastic properties at the nanoscale and microscale. Depending on the applied peak load, indentation techniques can either characterize the mechanical properties of individual mineral phases within the shale or reflect the bulk mechanical response of the composite rock matrix. In this study, dot matrix indentation tests were performed both by microindentation and nanoindentation on organic-rich shale specimens obtained from different stratigraphic intervals of the Bakken shale formation in the Williston Basin, North Dakota, USA. Microindentation was used to evaluate the bulk mechanical response over regions that span multiple mineral phases, thereby capturing the mesoscale behavior of the composite shale material. In contrast, nanoindentation was used to investigate the localized mechanical properties, including hardness and elastic modulus of individual mineral phases within the shale matrix. The mineral composition, microtexture, and pore structure of the samples were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), and mercury intrusion porosimetry (MIP). The 2D finite element method (FEM) was used to upscale the mechanical properties of shale rocks from nanoscale to mesoscale and contrasted the moduli measured from microindentation experiments with those upscaled from the rock mineralogical method and nanoindentation methodology. The findings demonstrated that the shale samples from various locations had varying mineral compositions. The hardness and fracture toughness are positively connected with Young’s modulus. The upscaled Young’s modulus determined by the 2D FEM was slightly higher than the experimentally measured value, with a difference of approximately 5.5 GPa. The possible reasons for this discrepancy are discussed in detail.