Rock shelters in the central Saharan massifs preserve anthropogenic stratigraphic sequences that represent both a precious archive for the prehistory of the region and a powerful proxy data for Holocene palaeoenvironments. The geoarchaeological (micro morphology) and archaeobotanical (pollen analysis) approaches were integrated to investigate the anthropogenic sedimentary sequence preserved within the Takarkori rock shelter, a Holocene archaeological site located in the Libyan central Sahara (southern Tadrart Acacus massif). The site was occupied throughout the Early and Middle Holocene (African Humid Period) by groups of hunter-gatherers before and by pastoral communities later. The investigation on the inner part of the sequence allows to recognize the anthropogenic contribution to sedimentation process, and to reconstruct the major changes in the Holocene climate. At the bottom of the stratigraphic sequence, evidence for the earliest frequentation of the site by hunters and gatherers has been recognized; it is dated to c. 10,170 cal yr BP and is characterized by high availability of water, freshwater habitats and sparsely wooded savannah vegetation. A second Early Holocene occupation ended at c. 8180 cal yr BP; this phase is marked by increased aridity: sediments progressively richer in organics, testifying to a more intense occupation of the site, and pollen spectra indicating a decrease of grassland and the spreading of cattails, which followed a general lowering of lake level or widening of shallow water marginal habitats near the site. After this period, a new occupational phase is dated between c. 8180 and 5610 cal yr BP; this period saw the beginning of the frequentation of pastoral groups and is marked by an important change in the forming processes of the sequence. Sediments and pollen spectra confirm a new increase in water availability, which led to a change in the landscape surrounding the Takarkori rock shelter with the spreading of water bodies. The upper part of the sequence, dating between c. 5700 and 4650 cal yr BP records a significant environmental instability towards dryer climatic conditions, consistent with the end of the African Humid Period. Though some freshwater habitats were still present, increasing aridity pushed the expansion of the dry savannah. The final transition to arid conditions is indicated by the preservation of ovicaprines dung layers at the top of the sequence together with sandstone blocks collapsed from the shelter's vault. On the contrary, the outer part of the sequence preserves a significantly different palaeoenvironmental signal; in fact, the surface was exposed to rainfall and a complex pedogenetic evolution of the sequence occurred, encompassing the formation of an argillic laminar horizon at the topsoil, the evolution of a desert pavement, and the deposition of Mn-rich rock varnish on stones. These processes are an effect of the general environmental instability that occurred in the central Sahara since the Middle Holocene transition. Finally, the local palaeoclimatic significance of the sequence fits well with Holocene regional and continental environmental changes recorded by many palaeohydrological records from North Africa. This highlights the potential of geoarchaeological and archaeobotanical investigations in interpreting the palaeoenvironmental significance of anthropogenic cave sediments in arid lands.