Purification protocols to extract pollen from lake sediments contain chemicals that 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. Pollen of broad‐leaved and coniferous trees reacted differently to chemical exposure, but response patterns are generally alike. Alterations of δ13Cpollen values vary between + 1.0‰ (B. pendula, NaClO‐treatment) and −5.0‰ (P. sylvestris, H2SO4‐treatment). The δ13Cpollen values of raw and chemically treated samples seem to be related after treatments with KOH, NaClO and HF, whereas the application of H2SO4 led to inconsistent changes among species. 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). In general, the use of isotope‐altering chemicals in purification protocols should be brought to a minimum, but the application of KOH and NaClO seems mostly unproblematic before δ13Cpollen and δ18Opollen analysis.