* 1991–1995 – Presidential Young Investigator Award;
* 1991 – Alfred P. Sloan Foundation fellowship;
* 1991 – ACS Exxon Solid State Chemistry Fellowship;
* 1994 – Coblentz Award for Advances in Molecular Spectroscopy;
* 1994 – Wilson Prize at Harvard;
* 1994 – Department of Energy Award for Outstanding Scientific Accomplishment in Materials Chemistry;
* 1995 – Materials Research Society Outstanding Young Investigator Award;
* 1997 – Department of Energy Award for Sustained Outstanding Research in Materials Chemistry;
* 2005 – Colloid and Surface Chemistry American Chemical Society Award;
* 2006 – E. O. Lawrence Award;
* 2006 – Eni Italgas prize for Energy and Environment;
* 2006 – The Rank Prize (Optoelectronics);
* 2006 – University of Chicago's Distinguished Alumni Award (Professional Achievement);
* 2008 – Kavli Distinguished Lectureship in Nanoscience, Materials Research Society;
* 2009 – Nanoscience Prize, International Society for Nanoscale Science, Computation & Engineering;
* 2010 – Medaglia teresiana, University of Pavia;
* 2011 – Linus Pauling Award;
* 2011 – Von Hippel Award, Materials Research Society;
* 2012 – Wolf Prize in Chemistry;
* 2014 – National Medal of Science;
* 2014 – ACS Award in the Chemistry of Materials;
* 2015 – Axion Award, Hellenic American Professional Society;
* 2015 – Spiers Memorial Award, Royal Society of Chemistry;
* 2016 – Dan David Prize for nanoscience research;
* 2017 – NAS Award in Chemical Sciences;
* 2019 – Welch Award in Chemistry;
* 2020 – BBVA Foundation Frontiers of Knowledge Award;
* 2021 – Priestley Medal;
In addition to those listed above, Alivisatos has held fellowships with the American Association for the Advancement of Science, the American Physical Society (1996), and the American Chemical Society. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences.