His research has enabled real-time observation of atomic motions in materials during chemical processes and has shed light on the structure-function correlation that underlies biology.

Following graduation, Miller gained a faculty position at the University of Rochester and immediately took a 12-month leave to do postdoctoral research in solid state physics as a NATO science fellow at the Laboratoire de Spectrometrie Physique (renamed to Laboratoire Interdisciplinaire de Physique in 2011[13]) at the Université Joseph Fourier in Grenoble, France under the direction of Hans Peter Trommsdorff and Robert Romenstain.

In 1995, he moved back to Canada and relocated his research group to the departments of chemistry and physics at the University of Toronto.

From 2010-2014, R. J. D. Miller was the director of the Max Planck Group, Centre for Free Electron Laser Science/DESY, University of Hamburg.

From 2014-2020, he was the co-founding director of Max Planck Institute for the Structure and Dynamics of Matter (MPSD) in Hamburg, Germany.