* 2015	elected board member, European Academy of Microbiology (EAM)
* 2013	elected member, European Academy of Microbiology (EAM)
* 2012	iGEM Team Groningen: European and World Champion 2012 (Kuipers was supervisor/coach/coordinator of the iGEM team Groningen from 2008-2015)
* 2011	elected member, Royal Netherlands Academy of Arts and Sciences (KNAW)
* 2011	Simon Stevin Meester Award (Science and Technology Award of STW, NWO, the Netherlands) €500,000