Agro-pastoral activities in the past act as environmental legacy and have shaped the current cultural landscape in the European Alps. This study reports about prehistoric fire incidents and their impact on the flora and vegetation near the village of Ardez in the Lower Engadine Valley (Switzerland) since the Late Neolithic Period. Pollen, charcoal particles and non-pollen palynomorphs preserved in the Saglias and Cutüra peat bog stratigraphies were quantified and the results compared with the regional archaeological evidence. Anthropogenic deforestation using fire started around 4850 cal. BP at Saglias and aimed at establishing first cultivated crop fields (e.g. cereals) and small pastoral areas as implied by the positive correlation coefficients between charcoal particles and cultural and pastoral pollen indicators, as well as spores of coprophilous fungi. Pressure on the natural environment by humans and livestock continued until 3650 cal. BP and was followed by reforestation processes until 3400 cal. BP because of climatic deterioration. Thereafter, a new, continuous cultivation/pastoral phase was recorded for the Middle to Late Bronze Age (3400–2800 cal. BP). After rather minor human impact during the Iron Age and Roman Period, intensive agriculture was recorded for the Medieval Period. The area around Ardez was used for crop cultivation from about 1000 cal. BP until the start of the ‘Little Ice Age’ (600 cal. BP). Despite a land-use reorganisation, the following gradual decrease in agricultural activities led to the extant mixture of a cultivated, grazed and forested landscape in the Lower Engadine. In addition, this study demonstrates the excellent value of the fungus Gelasinospora as a highly local marker of past and today’s fire incidents, as well as of the use of micro-charcoals from pollen slides and macrocharcoals (>150 μm) from pollen sample residues for the reconstruction of short- and long-term fire histories.