Abstract Centuries of human interference have led to large scale reduction of montane forests in the northern Ecuadorian Andes. As a result the natural position of the upper forest line (UFL) in the area is now subject of scientific debate, which is hindering sustainable reforestation efforts. Uncertainty is fuelled by insufficient precision of fossil pollen spectra to reconstruct the natural UFL position. Here we tried to resolve this issue by using biomarkers, i.e. plant species specific patterns of n-alkanes and n-alcohols, preserved in soils in the northern Ecuadorian Andes as additional proxy to reconstruct the natural UFL position. To unravel preserved biomarker patterns we used the recently developed VERHIB model, and for the first time assessed its applicability in soil archives. Changes in Holocene biomarker-based vegetation composition were directly compared to changes in pollen-based vegetation composition from the same soil profiles. Both proxies proved to be complementary and a combined application allowed for a more accurate reconstruction of past vegetation than with pollen analysis alone. We found that the present-day UFL in the study area has not been significantly depressed by human interference and was at 3650m maximally during late Holocene times. For the moment of post-glacial forest development we found a migration lag between pollen (earlier) and biomarkers (later). This reflects the difference between the non-transported biomarker signal showing spot-dating (thus in paleoecological studies functionally equalling the information from plant macro-remains in peat bogs), and the upslope wind-blown pollen signal showing an upslope forest expansion up to over a millennium ahead. The combined pollen-biomarker approach in soil cores shows great potential for vegetation reconstruction. However, more research of biomarker consistency and preservation is needed before application in other environments.