We present a multiproxy characterization of a complex, polycyclic soil sequence from Les Alcusses, Moixent (Valencia, SE Spain). The area has abundant settlements dating from early Neolithic to Roman times. The sequence comprises six main units, dating back to 8.7–8.5 ka cal BP. We integrated mineralogy, inorganic (pH, grain size, elemental composition) and organic chemistry (pyrolysis gas chromatography/mass spectrometry, pyrolysis–GC/MS), micro-charcoal, pollen and non-pollen palynomorph (NPP) data. All data is contextualized within a framework of archaeological information and radiocarbon dating, with the aim of deciphering the Holocene environmental changes.We infer a shift from wetter and warmer, in the early-mid Holocene, to drier and cooler climatic conditions with increased fire occurrence, in the mid-late Holocene (particularly after 5.3 ka cal BP). Although the pollen record indicates a rapid forest retreat and expansion of grasslands for the Neolithic period, local proxies (molecular soil OM indicators and NPP) point to the presence of pine forest in the studied location well after the regional decline started. The same proxies suggest a sharp forest decline after about 7.0 ka cal BP. Strong soil erosion, likely linked both to climatic instability and the intensification of human exploitation, resulted in a hiatus from the late Neolithic to the Roman period. A certain climate amelioration, wetter conditions and land abandonment or, at least, lower human pressure, are suggested for the late Roman period/Early Middle Ages. Direct evidence of changes in soil properties due to agriculture was not detected in the sequence except for the upper soil unit studied, which reflects intense agricultural management (with the possible use of agrochemicals).