The study presents the combined results of wood charcoal and phytolith analysis at Alepotrypa Cave, southern Peloponnese, Greece. The cave preserves rich cultural remains (hearth and floor constructions, pits and platforms, human bone scatters, massive quantities of fine pottery, lithic artefacts and ornaments) spanning the late Early to the Final Neolithic. The studied macro and micro-remains come from two distinct areas of the cave, the anterior chamber (close to the entrance of the cave) and the interior chambers (including a small fresh water lake), which, as has been suggested by several lines of evidence (analyses of cultural remains, human bones and micromorphology), were used for domestic and ritualistic purposes respectively. The aim of this study is two-fold: a) to investigate the local vegetation, and woodland management, b) to understand the use of plants and use of space along the habitation history of the cave exploring the possibility of a domestic setting for the anterior chamber and a ritualistic one for the interior. Wood charcoal and phytolith analyses support the two modes of usage; different fuel types in the hearths of the interior and anterior chambers of the cave along with different activities are documented. The anterior preserves well prepared clay floors and platforms with some cereal remains indicating light processing or consumption. The hearths in this area were fed with leafy branches from the open vegetation of the surrounding rocky slopes that included various scrub plants and scattered drought-resistant trees. Τhrough time and probably as a response to increased demand due to more frequent and longer-lasting use of the cave, neolithic people expanded their fuel-procurement activities to nearby evergreen woodland and deciduous oak thickets. By contrast the interior preserves evidence of ritualistic activities supported by the use of selected types of fuel, i.e. composted sheep dung along with firewood from scrub vegetation and small diameter wood of Fabaceae, Cistus sp. and Phillyrea/Rhamnus alaternus. The excellent burning qualities of composted dung and the ease of transportation of such material as well as of the small size firewood would explain their preferential use in the interior chambers where access was exceptionally difficult. Nevertheless, the slow-burning glow and smell of dung under the light of Pinus nigra resinous wood torches may have enhanced the powerfully evocative atmosphere of the interior chambers serving ritual purposes.