Achanurangatha Veedu movie tells the story of Prabhakaran (Salim Kumar) who is a student of Marthoma College, Thiruvalla, who falls deeply in love with Lillikutty (Usha) who is a Christian girl and marries her against the wishes of his family and converts to Christianity.
Lillikutty dies after the birth of their third daughter, and Prabhakaran now Samuel, is burdened with bringing up the children single handedly. The eldest daughter Treesa (Suja Karthika) who is married off to what turns out to be a good for nothing son-in-law, played to perfection by Harisree Ashokan (Josekutty). The second daughter Shirley burdened with family chores discontinues her studies.
Samuel pins his hopes on his third daughter Lissamma (Mukhta) and dreams of grooming her to be a doctor. But she is caught in a sex racket.