In 1988, he joined the Lunar and Planetary Institute (Houston, TX, USA) and the NASA Johnson Space Center for half a year as a Fulbright Scholar.

In 2007, he received the Barringer Medal of the Meteoritical Society, its highest award for research related to impact cratering studies.

Köberl's research activities center around two main themes: the investigation of impact cratering related processes and rocks through detailed and multidisciplinary investigations (mainly using geochemistry, petrography, and mineralogy, but also field geology and geophysics), as well as the development and testing of new methods that can be applied for such studies.

Additional research interests include investigations of terrestrial mass extinction horizons (including the late Eocene, K-Pg, Tr-J, and P-Tr strata), of meteorites and lunar rocks, Antarctic meteorite field studies, snowball earth, and several other geochemistry-related issues.

He has organized several international research conferences, including the Annual Meeting of the Meteoritical Society in 1989 in Vienna, Austria; the meeting on Catastrophic Events & Mass Extinctions: Impacts and Beyond, in 2000 in Vienna, Austria; Geological Society of America Field Forum on "Bolide Impacts on Wet Targets" in Nevada and Utah, USA; and the Geological Society of America Penrose Conference on "Hothouse, Icehouse, and Impacts: The Late Eocene Earth" at Monte Conero in Italy.

In his capacity as director general of the Natural History Museum in Vienna, Köberl is planning to increase the quality and visibility of research at the museum, to provide a larger number and greater variation of special exhibitions covering modern natural sciences, and to renovate and update the permanent exhibitions.