Hammes-Schiffer is a Fellow of the American Physical Society (2010), the 
American Chemical Society (2011), the American Academy of Arts and Sciences (2012), the American Association for the Advancement of Science  (2013), the National Academy of Sciences (2013), and the Biophysical Society (2015).  She was elected as a member of the International Academy of Quantum Molecular Science in 2014.
Hammes-Schiffer has received a number of awards, including the following: 
* 1996, Faculty Early Career Development (CAREER) Award, National Science Foundation (NSF), for her work on "The Incorporation of Quantum Effects in the Simulation of Proton Transfer Reactions"
* 2005, Iota Sigma Pi Agnes Fay Morgan Research Award
* 2005, International Academy of Quantum Molecular Science Medal
* 2008, American Chemical Society Akron Section Award
* 2011, "Method to Extend Research in Time" (MERIT) award, National Institutes of Health (NIH), a 10-year research grant to support her work
* 2020, Bourke Award of the Royal Society of Chemistry
*2021, American Chemical Society Award in Theoretical Chemistry
*2021, Willard Gibbs Medal Award from American Chemical Society Chicago Section