In 2005, Dauphas was awarded Nier Prize of the Meteoritical Society which recognizes outstanding research in meteoritics and closely allied fields by young scientists. In 2007, he was awarded the David and Lucile Packard Foundation Fellowship, given to the most promising early-career scientists and engineers, across the US. He won the 2008 Houtermans Award, given by the European Association of Geochemistry for outstanding contributions to geochemistry. He was awarded the James B. Macelwane Medal of the American Geophysical Union (AGU) for "significant contributions to the geophysical sciences", and was selected as an AGU Fellow in 2011. In 2014, he became a Fellow of the Meteoritical Society. He was one of the finalists in 2017 for the Blavatnik National Awards.
In 2016, Dauphas received a named professorship from the University of Chicago  as the Louis Block professor, Physical Sciences Division. In 2019, Dauphas was elected Geochemical Fellow of the Geochemical Society and the European Association of Geochemistry in recognition of his career contribution to the field of geochemistry.