| WARF Romnes Faculty Fellowship, University of Wisconsin-Madison | Joshua J. Coon |
| Biemann Medal, American Society for Mass Spectrometry | Joshua J. Coon |
| Arthur F. Findeis Award for Achievements by a Young Analytical Scientist, American Chemical Society | Joshua J. Coon |
| Pittsburgh Conference Achievement Award | Joshua J. Coon |
| Philip R. Certain Dean's Distinguished Faculty Award | Joshua J. Coon |
| Ken Standing Award, University of Manitoba | Joshua J. Coon |
| National Science Foundation CAREER Award | Joshua J. Coon |
| Beckman Young Investigator Award | Joshua J. Coon |
| American Society of Mass Spectrometry Research Award | Joshua J. Coon |
| Eli Lilly and Company Young Investigator | Joshua J. Coon |
| Named one of Tomorrow's PIs by Genome Technology magazine | Joshua J. Coon |
| Ruth L. Kirchstein Individual National Research Service Award (NIH-NRSA) | Joshua J. Coon |