The paper reports a revision of the tectonic-depositional evolution of the continental Cinigiano-Baccinello and Velona basins, located in the Amiata Volcano region, with special emphasis on the Messinian dynamics. Integration of facies analysis, magnetostratigraphy, and structural geology allowed a comparison of the evolution of these basins and a discussion of possible local to regional implications. At a local scale, crustal shortening, accommodated by thrust faults and related anticlines delimiting the basins, determined a dynamic physiographic and hydrographic scenario during the Messinian. Uplift of the tectonically-controlled shoulders was paired with pulses of subsidence in the basins that favoured the development of palustrine-lacustrine settings or endorheic alluvial plains. Stages of quiescent tectonics favoured fluvial incision of structural thresholds and the development of a south-directed drainage system, particularly developed during the late Messinian in coincidence with the Mediterranean Messinian Salinity Crisis. The dominant fluvial and clastic depositional pattern recorded in these basins during such a regional scale event points to local tectonic activity of the Northern Apennines playing a major role than the climatic, eustatic and geodynamic factors that controlled the Mediterranean region.