From 2008 the Estonian Journal of Ecology began its way in science publishing as an independent journal. However, this is not a fully new beginning, but a renovated and modernized continuation of the journal Proceedings of the Estonian Academy of Sciences: Biology Ecology.

The Estonian Academy of Sciences has been publishing the Proceedings of the Estonian Academy of Sciences for more than 50 years and the series Biology. Ecology since 1956. The series Biology. Ecology was internationally peer-reviewed and abstracted or indexed in several review journals and databases. The ties of succession between the two journals are stressed by continued volume numeration.

Estonian Journal of Ecology is published by the Estonian Academy of Sciences in collaboration with the University of Tartu, Tallinn University, Tallinn University of Technology and the Estonian University of Life Sciences. The journal is internationally peer-reviewed and is published in English with short abstracts in Estonian.

The Estonian Journal of Ecology invites original papers about biotic and abiotic environment, interactions between human and natural systems across temporal and spatial scales, in both terrestrial and aquatic ecosystems; past and future changes in the environmental quality; and sustainable use of environmental and renewable natural resources.