* 	Gruebele is a Member of the National Academy of Sciences (2013), a Member of the American Academy of Arts and Sciences (2010), and a Member of the German Academy of Sciences Leopoldina (2008).
* 	He is a Fellow of the American Chemical Society (2015), American Physical Society (2002), and the Biophysical Society (2005).
* 	Gruebele has received national and international awards, such as the Hans Neurath Award of the Protein Society (2020), TREE Award (Research Corporation, 2018)  the Nakanishi Prize (2017), the Raymond and Beverly Sackler Prize in the Physical Sciences (Tel Aviv University, 2008), the Friedrich Wilhelm Bessel Prize  (Alexander von Humboldt Foundation, 2005), and the Coblentz Award (Coblentz Society, 2000). He was also awarded an Alfred P. Sloan Fellowship (1997), a Cottrell Scholar Award from the Research Corporation  (1995), the Camille and Henry Dreyfus Fellowship  (1998, 1992), a David and Lucile Packard Fellowship (Packard Foundation, 1994),  a National Young Investigator Award (NSF, 1994), and a Beckman Fellowship, 1995–1996.
Gruebele collaborated with Hanoi University of Science to port the University of Illinois Department of Chemistry undergraduate curriculum for Chemistry to Vietnam. He has been on the list of "Teachers Ranked Excellent by their Students" at Illinois multiple times (most recently 2023), and received the School of Chemical Sciences Teaching Excellence Award. He is a contributor to LibreTexts, which makes open-access textbooks available to students.