Roshan was killed on 11 January 2012 by a motorbike bomb at 8:30am in the vicinity of Seyyed Khandan in Tehran. He was the last of four assassinated Iranian nuclear scientists.
In response to this and previous assassinations, a number of students from universities throughout the country sent letters to Iranian authorities, asking them to change the names of Iranian nuclear facilities and enrichment sites to those of the murdered scientists. Five of these requests were honored, and the Natanz enrichment site's name was changed to "The Site of Shahid Mostafa Ahmadi-Roshan".