Organic carbon and nitrogen fixed in illite (I) clays were identified in a hydrothermal breccia structure from the Harghita Bãi area of the Neogene volcanism of the East Carpathians. The potassium-illite (K-I) alteration related to an early magmatic-hydrothermal event (9.5 ± 0.5 Ma) was later replaced by ammonium-illite (NH4-I) (6.2 ± 0.6 Ma) owing to circulation of an organic-rich fluid. Several textural evolutions of breccia structures were recognized, such as ‘shingle’, ‘jigsaw’, ‘crackle’ and hydraulic in situ fractures. The high-field-strength element behaviours of the K-I and NH4-I argillic altered andesite are close to chondritic ratios, indicating no contribution of hydrothermal fluid, especially on NH4-I andesite alteration and the CHArge-and-RAdius-Controlled (CHARAC) behaviour within silicate melts. The rare earth element normalized patterns show two distinct trends, one with a Eu* anomaly (K-I) and the other with a Nd* anomaly (NH4-I), indicating a boundary exchange with the organic-rich fluid. The strongly depleted δ13C (V-PDB) measured for the NH4-I clays reflects values (−24.39 to −26.67 ‰) close to CH4 thermogenic oxidation, whereas the δ15N (‰) from 4.8 to 14.8 (± 0.6) confirmed that the N2 originated from post-mature sedimentary organic matter. The last volcanism (6.3 to 3.9 ± 0.6 Ma) and simultaneous volcano-induced tectonics in the proximity of the eastern Transylvanian basin basement increased the heat flow, generating lateral salt extrusion, diapirism and increased pressure in the gas reservoir. New pathways were opened that provided new circulation routes for basinal fluids to new and old permeable zones and expelled seeps from the biogenic petroleum system.