Purification protocols to extract pollen from lake sediments contain chemicals, which alter the carbon and oxygen pollen-isotope values according to pollen characteristics and family affiliation. Modern (raw) pollen of broad-leaved (Alnus glutinosa, Betula pendula, Carpinus betulus, Corylus avellana, Fagus sylvatica and Quercus robur) and coniferous tree species (Picea abies and Pinus sylvestris) were treated with potassium hydroxide (KOH), hydrofluoric acid (HF), sodium hypochlorite (NaClO) and sulphuric acid (H2SO4) to test the impact on δ13Cpollen and δ18Opollen and assess the applicability in purification protocols. Alterations of δ13Cpollen values vary between +1.0‰ (B. pendula, NaClO-treatment) and -5.0‰ (P. sylvestris, H2SO4-treatment). The impact of chemicals on δ18Opollen are more diverse and offsets range between +1.1‰ (C. avellana, NaClO-treatment) and -17.9‰ (P. sylvestris, H2SO4-treatment). Pollen of broad-leaved and coniferous trees reacted differently to chemicals, but response patterns are generally alike. The usage of isotope-altering chemicals in purification protocols should be brought to a minimum, but the application of KOH and NaClO seems unproblematic.