Stefanie Pöggeler studied biology at the Ruhr University Bochum, where she completed her doctorate at the Chair of General and Molecular Botany under Ulrich Kück. During her doctoral thesis, she investigated intron-encoded reverse transcriptases and endonucleases from algae and fungi. After a stay abroad at the Université Paris Sud, she habilitated in 2000 on the regulation of sexual reproduction in fungi at the Ruhr University Bochum. After further work as a university lecturer in Bochum and a deputy professorship at the Westfälische Wilhelms University in Münster, she was appointed university professor in Göttingen in 2006.
She is head of the Department of Genetics of Eukaryotic Microorganisms at the Institute of Microbiology at the Georg-August University. Her research focuses on the fruiting body development of hyphal fungi. Her research focuses on genetic and cell biological work on autophagy and signal transduction. Her teaching focuses on genetics, microbial cell biology and biotechnology in the Bachelor's programs Biology, Biochemistry and Biodiversity as well as in the Master's programs Molecular Life Science, Molecular Biology, Computational Biology and Master of Education (Biology).