Dr Nielsen's primary research interest is in Egyptian archaeology and the material culture of New Kingdom and Late Period Egypt, with emphasis on ceramics and craft production. He also specialises in Egyptian settlement archaeology, in particular in the Delta and the Marmarican Coast. As part of this specialisation, he has conducted excavations at Tell Nabasha in the northeastern Nile Delta, and also works on a project focusing on the 1886 excavations of the site by the British archaeologist Flinders Petrie. In addition, he has published inscriptional material from various UK museum collections.
He also conducts pedagogical research, focusing in particular on the effective development of Distance Learning in Higher Education. He has recently co-written (with Professor Joyce Tyldesley) From Mummies to Microchips: A Case Study in Effective Online Teaching Developed at the University of Manchester published by Routledge.