In 2017 he was awarded the Erwin Schrödinger prize together within an interdisciplinary team at ETH Zürich. In 2021, Fabian Theis was honored with the Hamburg Science Award, the most highly endowed prize of a science academy in Germany. Fabian Theis is part of and also coordinates various consortia (i.e. sparse2big involving 8 Helmholtz Centers) and founded the network SingleCellOmics Germany (SCOG). Furthermore, he coordinates 2019 launched Munich School for Data Science (MUDS) and is co-directing the ELLIS Munich Unit, the local hub of the European Machine Learning network ELLIS. Since 2020, he has been co-chair of the Bavarian AI Council of the Bavarian Ministry for Science and Art and supports the TUM with his expertise as a start-up Ambassador and as a core member of the Munich Data Science Institute (MDSI).
Professor Dr. Dr. Fabian Theis receives one of the prestigious Advanced Grants from the European Research Council (ERC) for his project "DeepCell".

Additionally, Fabian Theis was accepted for membership in the European Molecular Biology Organization (EMBO) in July 2022 and was appointed to the Board of Directors of Human Cell Atlas, Inc.

Fabian Theis received one of the prestigious Advanced Grants from the European Research Council (ERC) for his project "DeepCell" as well as the Gottfried Wilhelm Leibniz Prize 2023 – the most prestigious research award in Germany.