The Lower Cretaceous Agrio Formation is a source rock considered to be a possible unconventional reservoir. However, no detailed microstructure characterization of this hydrocarbon play has been performed. An exceptional oil-prone level is determined through outcrop information, petrography, x-ray diffraction, geochemical analysis, and x-ray micro–computed tomography (µCT). Microscopic studies reveal a lenticular fabric and calcareous nannofossils suggesting high carbonate productivity in the water column and algal-derived organic matter. The high organic matter content points to anoxic–euxinic conditions consistent with pyrite framboids, authigenic fluorapatite, and an elevated concentration of redox-sensitive elements. However, burrows reveal the activity of infaunal organisms, thus rejecting the idea of persistent bottom-water anoxia. The bioturbated, calcareous plankton and carbonate-rich mudstone represents accumulation in a distal outer ramp setting with calcareous plankton blooms and the co-occurrence of benthic microbial mats. Bottom currents, probably as a consequence of storm-related processes, were involved in detrital transport and oxygenation pulses. A three-dimensional (3-D)–microstructure reconstruction reveals three main µCT density-dependent phases: (1) a low-density phase composed of organic matter and calcite, (2) an intermediate-density phase dominated by calcite and minor organic matter, and (3) a high-density phase composed of authigenic minerals (pyrite, marcasite, and fluorapatite) and silt-sized detrital quartz and plagioclase. This analysis showed that burial diagenesis did not create enough pore space to be evaluated through µCT and that besides mineralogy, particle-size distribution, particle arrangement (sorting), and the local compaction degree affect the 3-D reconstructed structure. The analyzed sample is located toward the carbonaceous end member of the shale spectrum and exemplifies new approaches for the characterization of carbonate oil shales in the unit and similar deposits. From the perspective of unconventional exploration, the evaluation of depositional and postdepositional controls on the resultant microstructure might contribute to a better understanding of potential target intervals within the Agrio Formation.