Bawendi was granted the Sloan Research Fellowship in 1994. He won the 1997 Nobel Signature Award for Graduate Education in Chemistry of American Chemical Society (ACS). In 2001, he received the Sackler Prize in Physical Chemistry of Advanced Materials. In 2006, he was awarded the Ernest Orlando Lawrence Award. 
He was elected member of the American Association for the Advancement of Science in 2003, of the American Academy of Arts and Sciences in 2004, and of the National Academy of Sciences in 2007.
In 2010 during the National Meeting on March 23, 2010, Bawendi received the ACS Award in Colloid and Surface Chemistry. He also received the 2011 SEMI Award for North America for quantum dot research.
Bawendi was selected as a Clarivate Citation Laureate in Chemistry in 2020, jointly with Christopher B. Murray and Hyeon Taeghwan, "for synthesis of nanocrystals with precise attributes for a wide range of applications in physical, biological, and medical systems." 
In 2023, Bawendi was awarded the Nobel Prize in Chemistry jointly with Louis E. Brus and Alexey Ekimov "for the discovery and synthesis of quantum dots".