Diebold's first appointment after graduation was as a post-doctoral research associate in the group of Theodore E. Madey in the department of physics at Rutgers University (1990-1993). It was there that she was first introduced to oxide surfaces, an area that she would later come to refer to as "the love of her scientific life".  Her first faculty appointment followed, at Tulane University, New Orleans, USA, where she was an assistant professor (1993–1999), associate professor (1999–2001), and professor of physics (2001–2009), and also an adjunct professor of chemistry (1993–2009). During this time period, she also completed her habilitation in experimental physics (TU Vienna, 1998), held the Yahoo! Founder Chair in Science and Engineering (2006–2009), and was the associate department chair (2002–2009).
In 2005, Diebold and her group were forced to temporarily evacuate from New Orleans, which experienced massive flooding and power outages from the impact of Hurricane Katrina. They were hosted by the group of Theodore E. Madey at Rutgers University during this challenging period.
In 2010 she moved to the Institute of Applied Physics at TU Wien where she is currently a professor of surface science and deputy department head, and retains the title of research professor at Tulane University.. Since 2022 she also serves as Vice President of the Austrian Academy of Sciences.