Fe–Mn concretions and mineralizations, associated with condensed horizons and hardground, are significant archives in ancient carbonate rocks. Their petro-chemical study allows an assessment of the palaeoenvironmental context in which they were formed also connected to their biotic or abiotic origin. At the western side of the Monte Inici (Fornazzo section, north-western Sicily) a well exposed outcrop of condensed pelagic limestones (Rosso Ammonitico facies: Middle‒Upper Jurassic) is well-known and thoroughly studied. In this section, the base of the Rosso Ammonitico facies consists of a very condensed level rich in fossils with a variable thickness deposited from the early Bathonian to the early/middle Callovian. It is characterized, at the top, by the noticeable presence of Fe–Mn concretions, typical of the Tethyan Jurassic and related to very low sedimentation rates. For this study, Fe–Mn crusts and mineralizations from the Fornazzo section were investigated using X-ray diffraction, scanning electron microscopy, X-ray fluorescence, ICP and stable-isotope mass spectrometry. The collected samples, deposited in submarine conditions (as testified by stable oxygen and carbon isotopes), have been subdivided in two typologies with different macroscopic and mineralogical features. The Fe–Mn crusts consist of hematite, todorokite and birnessite and are characterized by a relatively low Mn/Fe ratio. Their content in trace elements, rare earths and yttrium (REY) is compatible with a hydrogenetic origin involving the oxy-hydroxides colloids precipitation directly from seawater. Microbially mediated processes are here testified by the recognition of filamentous and coccoid-shaped microstructures referable to coexistence of chemosynthetic fungi and photosynthetic cyanobacteria and accounting for a deposition in the deep euphotic zone. An average growth rate of ~ 8.5 mm/Myr for the Fe–Mn crusts, estimated by cobalt concentrations, suggests a time elapsed for deposition of ~ 3.5 ± 1 Myr. This value is compatible with the stratigraphic gap embracing the time span from the early/middle Callovian to the middle Oxfordian. In the neighbouring pelagic limestones, Fe–Mn deposits are present in the form of micro-dendrites mainly consisting of pyrolusite, sometimes associated with carbonato-fluorapatite. The geochemical composition gives evidence of a prevalent early diagenetic origin with precipitation, at the sediment/water interface or in the first centimeters of sediments, of metals diffused from the crusts as consequence of fluctuating redox conditions. Although the well-preserved Frutexites texture is commonly related to a microbial activity, other bacterial microstructures have not been recognized, having probably been obliterated during the growth of the dendrites. Nevertheless, it is possible to suppose a deepening in the bathymetry consistent with the involvement of chemosynthetic microorganisms in the formation of Frutexites structures.