The scene with Keiichi discovering that Mion and Shion are separate people happens during festival preparations instead of at a store.
The scenes with Rika ranting to Keiichi and her subsequent disappearance are changed. In the manga, Rika goes home soon after Kiichirou is reported missing and rants to Keiichi when he tries to go home with her. Satoko later reports that Rika hasn't come home. The club searches near Rika's shack and find that Satoko is also missing.
In the climax, it is not shown who or what was invading the Sonozaki estate when Mion checks the cameras.
Vol 1: Nienagashi • Don't Quit, Chie-Sensei • Sukekomashi • Matsurinosonaemononokazarikowashi • The Girl's Lost Memories • Punishment Games are a Silver Bullet • Minaitoshi • Little Demon • The Melancholy of Stir-Fried Vegetables • Onidamashi Vol 2: Rika-Sato Wars • Hinageshi • Usomabushi • When the Bed-wetter Cries • Courtesy of a Bargain Sale Auction Event • Satokoishi • The Butterfly's Dream • A Fragmented Account Revealed by a Certain Scrapbook • Festival Accompaniment, Thereafter • The Illness at the End of the Hundredth Year's Rope • A Kyute Lesson from Hell Vol 3: Limit • Thank You • Feelings of that Day, Feelings at Present • Shion After • The Rustic Belle of Shishibone • "Welcome Home", "Goodbye" • The Cuckoo Clock and Dreams of a Loving Home • Kimodameshi • Keiichi's Confession Time Chapter • Catching the Northern Star • Jirou Tomitake Dies Twice • Yukiwatashi