The Institute of Biology is characterized by a lively exchange with other institutes of the BCP department and the Berlin research landscape. This is reflected in the participation in many interdisciplinary research alliances, such as excellence clusters, graduate schools, special research areas, research groups, Research Training Groups (GRKs), BMBF research alliances and priority programmes.

At the national level, there is close cooperation with external research institutions such as Helmholtz Centres, Leibniz and Max Planck Institutes and federal institutes (BAM, BfR, etc.). In addition, the institute cooperates in numerous projects with other Berlin universities, the University of Potsdam, the partner university LMU Munich and many other German universities.

One example is the Berlin-Brandenburg Institute for Biodiversity Research; an association of four universities (FU, UP, TU, HU) and five Leibniz Institutes (IGB, IZW, ZALF, MfN, PIK) with the aim of bridging the traditional boundaries in biodiversity research. Research at the Institute of Biology is also actively funded at the Collaborative Research Centre (CRC) 958, for which the Institute of Biology is the spokesperson. Ten research groups of the Institute of Biology are currently involved in CRC 958. The Institute also takes part in the "NeuroCure" excellence cluster and the "Dahlem Centre of Plant Sciences".

The Einstein Research Unit “Climate and Water under Change” (CliWaC) is a transdisciplinary research initiative of the Berlin University Alliance set up to address water-related risks under climate change. CliWaC will bring together the social and natural sciences as well as practical expertise from stakeholders to support the governance of mitigation and adaptation measures in response to climate change.

The consortium consists of 28 project leaders affiliated with the BUA members Freie Universität Berlin, Humboldt-Universität zu Berlin, Technische Universität Berlin, and Charité – Universitätsmedizin Berlin. External institutions such as the Leibniz Center for Agricultural Landscape Research and the Institute for Ecological Economy Research are also involved in the initiative. Prof. Dr. Britta Tietjen (Freie Universität Berlin) and Prof. Dr. Jörg Niewöhner (Humboldt-Universität zu Berlin) are spokespeople for the Einstein Research Unit.