There are various conflicts throughout I Know Why the Caged Bird Sings. One which every reader remembers is the abuse and rape of the author by her mother's partner, Mr. Freeman. Another is the fight between Marguerite and Dolores, which leads to the former sleeping in a junkyard for a month. While these conflicts are undoubtedly memorable and powerful, the conflict that pervades the book, making an appearance in almost every chapter, is the conflict between the author—as well as the wider Black community in which she lives—and white America.

The small town of Stamps, in which most of the story takes place, is so completely segregated that, on a normal day, a person from one race would not even catch a glimpse of anyone from the other. However, there is always the danger of hostile incursions. Early in the book, a white woman is attacked, and the Ku Klux Klan decide to take revenge against any Black man they can find. Uncle Willie has to hide for fear of his life, despite the fact that he could not possibly have been the attacker. On another occasion, Marguerite has severe toothache, but the only dentist in town is white, and he says that he would sooner put his hand "in a dog’s mouth than in a n----r’s." Such injuries and insults abound throughout the text, constantly reminding the reader of the racial conflict which plagues the author.