| 2014 | The Good Spy | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · History & Biography | |
| 2014 | The Good Spy: The Life and Death of Robert Ames | Chicago Public Library Best of the Best source ↗ (opens in a new tab) | Selection · Best Books: More Nonfiction | |
| 2014 | The Good Spy: The Life And Death Of Robert Ames | NPR Books We Love source ↗ (opens in a new tab) | Selection · Books We Love | |
| 2014 | The Good Spy: The Life and Death of Robert Ames | Washington Post Best Books of the Year source ↗ (opens in a new tab) | Selection · Notable Nonfiction | |
| 2011 | Crossing Mandelbaum Gate | Dayton Literary Peace Prize source ↗ (opens in a new tab) | Finalist · Nonfiction | |
| 2010 | Crossing Mandelbaum Gate: Coming of Age Between the Arabs and Israelis, 1956–1978 | National Book Critics Circle Awards source ↗ (opens in a new tab) | Finalist · Autobiography | |
| 2006 | American Prometheus: The Triumph and Tragedy of J. Robert Oppenheimer | Pulitzer Prize (Biography and History) source ↗ (opens in a new tab) | Winner · Biography or Autobiography | |
| 2006 | American Prometheus: The Triumph and Tragedy of J. Robert Oppenheimer | J. Anthony Lukas Book Prize Project source ↗ (opens in a new tab) | Finalist · J. Anthony Lukas Book Prize | |