X-ray micro-computed tomography (microCT) is a non-destructive powerful tool for the analysis of microstructural features of geological materials. In the case of shales, a 3D visualization offers important information on the spatial distribution of organic components, inorganic phase minerals and if it is possible to get a description about pore space and microfractures. Given the internal complexity and heterogeneity of shales, microCT studies should be complemented by additional methods including bulk rock properties and microscopical observations to better understand the internal microstructure. The Meso-Cenozoic Neuquén Basin is renowned for its various petroleum systems and in recent years for its excellent unconventional oil and gas reservoirs. However, detailed studies on the microstructure of shales are poorlyreported in the literature. In this work, we analyzed an oil-prone shale level form the lowermost part of the Agua de la Mula Member (Agrio Formation) combining outcrop information, optical and electron microscopy, X-ray diffraction (XRD), X-ray microtomography (microCT), in addition to total organic carbon (TOC)-Rock Eval pyrolysis. This organic-rich shale (16.5% TOC) was accumulated in a distal outer ramp setting with calcareous microfossils and algal-derived organic matter that suggest high carbonate productivity in the water column related to plankton blooms and the co-occurrence of benthic microbial mats.These components are organized into very thin (< 10 mm) beds bounded by subtle erosional microsurfaces. The microCT results discriminate between units rich or depleted in organic matter proving its successful application for 3D microstructure reconstructions. This analysis showed that burial diagenesis did not create enough pore space to be evaluated through microCT and that, besides density and atomic number (mineralogy), the particle-size distribution, particle arrangement and local compaction degree might affect the reconstruction of a 3D image. The case study is an example of the new research approaches needed to understand the internal microstructure in unconventional carbonate reservoir/source rocks.