Hearth-pits are some of the most common archaeological features documented in open-air Mesolithic sites, especially in coversand areas of NW Europe. However, very few geoarchaeological studies have addressed their formation, function and relationship with occupation surfaces. This work introduces new interdisciplinary investigations on the sediments of the Mesolithic open-air site of El Arenal de la Virgen (SE Iberia). A selection of five hearth-pits from two different occupation phases (Phase 1: 9.3–9.1 cal ka BP and Phase 2: 8.6–8.3 cal ka BP) has been analysed using stratigraphy, texture, soil chemistry, micromorphology, petrography and OSL and TL analyses. Combustion traits of the carbonate rock assemblages preserved in the sediments of the hearth-pits have also been investigated and compared to reference and experimental data from local geogenic materials. Our results allowed us to discuss the anthropogenic origin and taphonomy of the hearth-pits studied and approach their function. The structures from Phase 1 are interpreted as a possible oven and a dumping feature linked to single/occasional use events. In contrast, for hearth-pits from Phase 2, we propose they were related to combustion and dwelling areas subject to recurrent occupation episodes and disturbance. Finally, our sedimentary and soil data revealed existing favourable paleoenvironmental conditions during the Mesolithic occupation of the site characterized by increased moisture, temperature and vegetation cover, in contrast to the Pleistocene and Middle Holocene periods pre- and post-dating the human settlement. This work highlights the potential of integrating geoarchaeological and contextual evidence to clarify the factors involved in the formation of hearth-pits and infer intra-site occupation patterns.Supplementary informationThe online version contains supplementary material available at 10.1007/s12520-023-01794-5.