Eocene flint 48–56.0 million years old (mya) from the Negev desert (Israel) was characterized using a suite of analytical techniques. High-resolution transmission electron microscopy (HR-TEM) and selected area electron diffraction (SAED) of the inorganic component showed the texture, morphology, size, and distribution of two silica polymorphs: α–quartz and moganite. While euhedral forms were attributed to α-quartz, moganite crystals were comprised of spherulitic grains. An electron less-dense amorphous material (no scattering under SAED) was found between the siliceous crystallites. Energy dispersive X-rays (EDS) and electron energy loss spectroscopy (EELS) demonstrated that this electron less-dense amorphous material is composed solely of carbon. Low vacuum, low energy backscattered environmental scanning electron microscopy (BSE-eSEM) imaging of flint surfaces showed the presence of micrometer-sized organic inclusions randomly distributed throughout the siliceous matrix. Energy-dispersive X-ray studies (EDS) demonstrated that these organic micro-inclusions were composed of carbon, sulfur, and nitrogen with a C/N ratio attributed to marine sources. These micro-inclusions were not directly associated with hard-shell fossils. BSE-eSEM imaging conditions allowed the identification of entrapped carbon-rich organic material, which is not possible when applying commonly used electron microscopy conditions that require carbon coating and high acceleration voltages, rendering carbon-rich features electron-transparent. Phase contrast-enhanced micro-computed tomography (PC-μCT) showed that these organic micro-inclusions were randomly distributed throughout the siliceous matrix.Time-of-flight secondary ion mass spectrometry (ToF-SIMS), nano-Fourier transform infrared spectroscopy (nano-FTIR), and scanning probe microscopy (SPM) were used to further characterize these organic micro-inclusions. These three in situ analytical techniques with nanometer resolution provided complementary information on the chemical composition and structure of the organic material. Specifically, ToF-SIMS analysis revealed amino acid and hydrocarbon mass spectra fingerprints inside the organic micro-inclusions. While the former were exclusively found in the organic micro-inclusions, the mass spectral fingerprints for hydrocarbons were also found in the siliceous matrix in agreement with the HR-TEM/EDS/EELS results, where pure carbon was found between the siliceous nanocrystals. While ToF-SIMS provides chemical information, it does not provide structural information. Nano-FTIR analysis showed the presence of amide I and II infrared vibrations exclusively on the organic micro-inclusions. The scanning probe microscopy (SPM) techniques Peak Force Quantitative Nanomechanics (PF-QNM) and Contact Resonance Atomic Force Microscopy (CR-AFM) were used to assess the mechanical properties. PF-QNM measurements on the organic micro-inclusions, under dry and liquid conditions, demonstrated that the organic micro-inclusions swell upon hydration and soften, pointing toward the presence of hydrophilic molecules in agreement with nano-FTIR and ToF-SIMS results. CR-AFM allows in situ determination of the mechanical properties of materials with high stiffness at nanometer resolution. This technique, rarely used in a geological context, revealed that the organic micro-inclusions had an unusually high stiffness atypical for modern organic material, which was attributed to molecular cross-linking promoted by diagenesis.This work provided a comprehensive view of the inorganic and organic components of Eocene flint from the Negev desert with implications for paleontology and archaeology. It offers a roadmap of novel complementary techniques that can be used in the exploration of entrapped organic material in flint.