Where the Lilies Bloom is the story of the Luther family who, following the death of family patriarch Roy, are left orphaned. The second-eldest daughter, Mary Call, is left to care for her siblings and protect the secret of her father's death so that the family will not be broken up. Mary Call struggles with her sudden responsibilities and with the pressures of outside interests and her own passion for writing. In the end she is able to keep her family together with the aid of a sympathetic landlord.
The Luther family are poor sharecroppers living in the mountains of North Carolina. The father, Roy Luther (Rance Howard) is sickly and asks the second eldest daughter, Mary Call (Julie Gholson) to take over his role of father when he passes on. He instructs her not to tell anyone when he dies as doctors, undertakers and preachers "just take money." When the authorities discover he is dead, the children will be split up and put in foster homes since none of them are of legal age.
Their landlord Kiser Pease, (Harry Dean Stanton), is interested in marrying the eldest daughter Devola (Jan Smithers). Roy Luther won't allow the marriage and makes Mary Call promise she won't let it happen after he dies. Mary Call and younger brother Romey (Matthew Burrill) help Kiser when he is sick with pneumonia and Kiser agrees to sign the land back over to the Luther family.
When Roy Luther dies, the children bury him on a mountain side in an unmarked grave, then go to elaborate lengths to keep anyone from finding out he is dead. The children rehearse over and over about what to say if asked about their father. Kiser continues his courtship of Devola with Mary Call doing everything she can to thwart his pursuit of her.
The Luther children scrimp and do all they can to eke out a living for themselves and even sell roots and herbs gathered from their land to the local pharmacist to use in medicines. Mary Call takes refuge in her journal, and the essays she writes for school assignments catch the eye of her teacher who urges her not to waste her talent with words by settling for "a life in the hills."
When Kiser lands in the hospital after having been hit by a truck, his nosy sister Goldie comes to the Luther house and demands they vacate the property. She says the paper that Kiser signed giving the Luthers back their land is worthless and orders them out in 48 hours. With no options left, a desperate Mary Call visits Kiser in the hospital and offers herself to him in marriage. Kiser would rather marry Devola and a distraught Mary Call blurts out that Roy Luther is dead. She threatens to kill Kiser if he tells anyone and storms out.
Finally, Mary Call agrees to let Kiser marry Devola. Mary Call realizes that Kiser was not so bad. After Kiser and Devola marry, the entire Luther family live together in Kiser and Devola's home.