The Pliocene cold‐seep carbonate of the Crotone Basin (South Italy) represents a key site for dimension, outcropping exposure and quality. These deposits form a large carbonate (calcite) body (350 m long, 100 m wide and 40 m thick), and are characterized by a conduit facies made of authigenic calcite interpreted as previously active gas/fluid escape pipes and by a pavement facies, depicted as the surrounding early calcite‐cemented bioclastic and siliciclastic sediments. Pavement facies are commonly colonized by chemosymbiotic and non‐chemosymbiotic macrofauna (Lucinid and Solemyid bivalves, gastropods and serpulids). The conduit microfacies is characterized by the inward accretion of dark micritic laminae alternating with whitish sparitic layers. The micritic laminae show a microbial peloidal to dendrolitic fabric, which commonly incorporates planktonic foraminifera and coprolites, whereas the crystalline layers consist of microsparitic and sparitic crusts of prismatic zoned calcite crystals. The pavement facies shows more variability, because it is typified by laminated microbial boundstones, chemosymbiotic–bivalves packstone, foraminiferal packstone/wackestone and hybrid arenites. The stratigraphic constraint coupled with the foraminiferal assemblage (planktonic taxa) suggest a deep‐water setting occasionally affected by siliciclastic sedimentary flows. The pavement facies also shows common brecciation features, suggesting the establishment of post‐depositional overpressure conditions due to the early cementation of the conduits, which triggered localized rock failure. Stable isotope analysis of the different facies reveals overall negative δ13C values (−6.8 to −37.4‰ Vienna PeeDee Belemnite), indicating the presence of a complex mixture of methane with other hydrocarbons consumed microbially via anaerobic oxidation of methane; whereas δ18O is relatively positive (0.0 to 3.4‰ Vienna PeeDee Belemnite) suggesting the possible dehydration of clay minerals and/or destabilization of gas hydrates. This study, besides helping in the definition of the migration pathways and modality of accumulation of hydrocarbon‐rich fluids, can also help in building more and more realistic models for the complex genesis of cold‐seep carbonates.