The novel bears the name of its primary theme. Throughout the work, the reader can see the characters search for atonement. "I gave them happiness, but I was not so self-serving as to let them forgive me," Briony says at the end of the novel. Briony recognizes her sin (i.e., wrongfully accusing Robbie and ruining his and Cecilia's chance at a life together) and attempts to atone for it through writing her novel. She does not grant herself forgiveness, rather, she attempts to earn atonement through giving Robbie and Cecilia a life together in her writing.

Briony experiences a loss of childhood innocence when she witnesses the fountain scene between Robbie and Cecilia. "But she knew very well that if she had not stood when she did, the scene would still have happened, for it was not about her at all...This was not a fairy tale, this was the real, the adult world in which frogs did not address princesses...". Briony recognizes she is in the stage between childhood and adulthood and she can no longer dwell in a fantasy realm but must instead move on to reality. Lola and the twins are also experiencing a loss as their lives crash down around them due to their parents' divorce, and they are forced to live with the Tallises. Lola, however, experiences the most severe loss when she is raped by Paul Marshall. Through all of these experiences, the characters are forced to make a choice or recognize a new part of life, resulting in the irrevocable loss of innocence.