Bersama keluarga kelincinya, Peter meninggalkan kebun Thomas dan Bea dan pergi ke kota. Saat mereka mengalami masalah, Peter meminta bantuan dari kawan-kawan lama.
Dalam film yang memadukan aksi langsung dan CGI ini, si usil Peter Rabbit menghadapi musuh baru yang tangguh dalam perebutan sayur di kebun Tn. McGregor.
The story focuses on a family of anthropomorphic rabbits, the widowed mother rabbit cautioning her young against entering a vegetable garden grown by a man named Mr. McGregor, telling them: "your Father had an accident there; he was put in a pie by Mrs. McGregor". Whereas her three daughters obediently refrain from entering the garden, going down the lane to pick blackberries, her rebellious son Peter enters the garden to snack on some vegetables. Peter ends up eating more than is good for him and goes looking for parsley to cure his stomach ache.