Erik Jan de Boer's research focuses on characterizing pre-historical anthropogenic impact on the functioning of island ecosystems and the ecological consequences of extinction. As a paleoecologist ,he records long-term data of species responses to environmental change to study species survival mechanisms and predict future changes in biodiversity. He integrates different proxy records – pollen, macro-charcoal, diatoms, geochemistry, biomarkers, palaeontology, aDNA – to produce highly detailed reconstructions, quantify ecosystem impacts, and collates and manages large datasets to study larger-scale biogeography patterns.

At CREAF he is part of the TEMPOINVASION project which investigates the ecological background of species invasions in the historical past in coastal environments around the Iberian Peninsula. He is also a member of the ECR-funded TIMELINES Project.