Mickleburgh's most recent research focuses on improving the detection, excavation and documentation of clandestine mass graves through the innovative combination of 3D digital tools and actualistic forensic taphonomy. She leads the Mass Grave Project, an interdisciplinary and international taphonomic research project simulating small scale primary and secondary mass graves at the human taphonomy facility of the Forensic Anthropology Center at Texas State University. Besides 3D visualization methods, this project incorporates a variety of biomolecular, biogeochemical, geophysical and remote sensing techniques to improve methods of human identification and recovery or archaeological evidence from mass graves. Her research interests and expertise furthermore extend to sensory archaeology, ethics surrounding human remains in archaeology and museum contexts, and Caribbean archaeology.

Mickleburgh currently holds a position as Assistant Professor at the Amsterdam Centre for Ancient Studies and Archaeology (ACASA) at the University of Amsterdam, where she teaches digital and science-based archaeology at undergraduate and graduate levels. She is also the director of the 4D Research Lab (4DRL) at the Faculty of Humanities, University of Amsterdam: 4DRL works on the cutting edge of 3D visualization for archaeology and cultural heritage. The lab's research includes the development of virtual and augmented reality apps used for the interactive exploration of the material past. The lab holds a wide range of computing facilities, 3D scanners, and 3D modeling software, and has a team of technicians and researchers with a broad range of technical expertise in 3D visualization.