One day, Nazi police send a call-up notice for her father and her sister Margot for their deportation to a concentration camp. They flee to their hiding place, the Secret Annexe.
Another family, the Van Daans, arrive with their son Peter. Anne particularly dislikes the frivolous Mrs. Van Daan. She also complains that the grown-ups criticize her.
Anne tells Kitty that her Jewish friends are being taken away by the dozens. They are loaded into cattle trucks and sent to concentration camps.
Daddy gets sick, but they cannot call a doctor, since they are in hiding. Anne reads a book on puberty and longs to have her period. She does not like to say her prayers with Mummy, for she finds Mummy cold. She gets jealous of Margot sometimes.
They take in another person, Mr. Dussel. He is stubborn. Anne often feels guilty for being safe in hiding while her Jewish friends are probably suffering.
Anne feels frustrated that she is criticized so often. She still does not get along with Mrs. Van Daan, and still finds Mummy cold, refusing to pray with her, upsetting her greatly.
Anne cannot sleep because of the air raids, and they are eating terribly-dry bread and ersatz coffee for breakfast, spinach and rotten potatoes for dinner. Still, Anne feels lucky that they have food and shelter, that they are able to laugh at each other, and that they have books and a radio.
There is an announcement that Italy has surrendered. This gives them hope for peace.
Anne chronicles a day in the Secret Annexe, describing many of the activities and personalities of the people in the Annexe. Anne is so affected by the tension that at times she goes to bed crying. She longs for fresh air, and wishes that the darkness and cruelty of the war would subside so that they can find beauty and safety. She has a dream of one of her friends, and feels guilty. She hopes that she prays hard enough to save her friends and family.
She and Peter Van Daan develop a crush on each other. She remembers Peter Wessel, who she loved before going into hiding. They combine in her mind, and she feels intense longing. The grown-ups are critical of the relationship. Anne worries that she talks too much, but he likes her cheerfulness. She wants to help him overcome his loneliness.
She hears that they will be making a collection of diaries and letters after the war, and wants to publish her diary. She has faith that God will raise them out of suffering, and that one day, the world will learn from the Jews. She is often downcast, but never in despair.
She writes Daddy a letter about how he did not help her through her struggle to find herself, and he is so upset that she feels guilty and realizes that she was wrong.
They are horrified to hear about antisemitism in Holland. Sometimes they go hungry, but even at their worst, they still have hope and are able to find cheerful moments. On D-Day, the English land on the French coast. There is great discussion about the hope of liberation, and they have fresh courage and strength.
Anne celebrates her fifteenth birthday. She wishes she could look at nature more often, and not through a dirty window. Many cities have fallen to the Allies, and the mood is optimistic.
She becomes disappointed in Peter. She does not want him to lean on her. She wonders how she has held onto her ideals in the face of all the cruelty of war. She still believes that people are really good at heart. She has a deeper, purer side that no one knows. She worries that people think she is superficial.
With this, her diary ends, for on August 4, 1944, the Secret Annexe was raided and they were taken away to German and Dutch concentration camps.