- The video of the 1979 theatrical re-release cuts a further twenty minutes and runs 97 minutes. All songs are cut, except for "Portobello Road", "Beautiful Briny Sea" and some parts of "Substitutiary Locomotion". Other sequences are reduced (such as Professor Browne's wait at the train station) or cut altogether (such as the disappearance of the magical necklace).
- The Disney Channel, to commemorate the film's 25th Anniversary, once showed the 1996 139m restored print with a special introduction by Angela Lansbury.
- The Disney+ Version omits the subtitles for the German soldiers dialogue.
- There is one still-missing song that was intended to be in the film, entitled "A Step in the Right Direction." It would have occurred after Miss Price opened her package and found a broomstick. Disney could not locate any film footage of this number, but they found the audio tracks and still photographs of the number. The restoration team created a still-photo recreation to include as a supplement; it has appeared on most home video versions of the 139-minute cut. Because it was done on tape, it was decided audiences might find the switch from live action to still photos jarring. For this reason, it was left out of the film's reconstruction.
- During the dubbing process for the German version in the early '70s, it was decided to remove all scenes featuring Nazis. This version was also released on DVD and video.
- In 1996, in honor of the film's 25th anniversary, the film was restored to a length of 139 minutes, close to the originally intended length (the film had been cut to 117 minutes against the wishes of its makers before its premiere). This version has the following scenes reinstated:
- A guardsman named Mr. Widdenfield (played by Arthur Malet) harasses Captain Greer, while Mrs. Hobday tries to clear things out (leading into the song "The Old Home Guard").
- A Home Guard sergeant asking for permission to dismiss the marching parade (immediately after "The Old Home Guard" ends).
- Mr. Jelk tells Mrs. Hobday of his plans to buy Miss Price's house.
- At dinner time, Carrie tells Miss Price she and her brothers are orphans, while she explains what happened to their caretaker, Aunt Bessie.
- Miss Price notes mangelwurzel jam is available at the dinner table, and they say grace, as the children look disgusted at Miss Price's tastes in food.
- Miss Price tells the children no one has ever seen her workroom before.
- As Mr. Jelk brings a letter to Miss Price (the one that informs her the Emelius Browne Correspondence College of Witchcraft has closed), he tries to get into the house and talk to her, but she politely sends him away.
- When Miss Price asks Paul for the bedknob back to get to London, Charlie attempts to extort some money from her, but she rebuffs him.
- After "The Age of Not Believing," Paul tries to get the bed to fly, but Miss Price forgot to tell him to tell the knob where to take them.
- When the children find Mr. Browne on the streets of London, they take the bed with them and follow him.
- The entire song "With a Flair" and its lead-in, as well as Mr. Browne's subsequent offer to sell his magic props.
- When Miss Price says "we'd be delighted [to join Mr. Browne for luncheon]," Mr. Browne asks if the children belong to her.
- At the townhouse where Mr. Browne is staying, Miss Price explains to her what substitutiary locomotion is and why she wants the spell.
- The second nursery scene, in which Paul discovers the book "Isle of Naboombu," is put before "Eglantine", whereas it was formerly after it.
- The song "Eglantine" is restored to its entirety.
- The song "Portobello Road" is restored to its entirety, as its subsequent dance sequence. The main song adds a scene with a used clothing merchant and another scene where Charlie and Paul play cricket. In the dance, the Caribbean dance now precedes the Irish dance. Unlike the rest of the formerly cut scenes, the tail end of the Irish dance and the beginning of the dance's climax only existed as a faded work-print that had to be digitally scanned and cleaned before it could be brought back to a passable state.
- Mr. Browne tells Swinburne that the bed once belonged to royalty and is being offered to the Bookman as a present, while the children push the bed through the door.
- Mr. Browne rebuffs the Bookman's offer to swap sections of the book, but relents when he is threatened.
- A scene in the village store where Mrs. Hobday meets Mr. Browne and suggests he should marry Miss Price. Mr. Jelk walks in and overhears them.
- The song "Nobody's Problem's for Me" is reinstated after Mr. Browne leaves the house. No orchestral track existed, so the studio recorded a new one.
- In some versions of the film shown on TV in the UK, a scene was cut between the main characters return from the animated island and the first use of the substitutiary locomotion spell, which shows the medallion they stole from the King disappearing, and then them realizing they could still get the complete spell from the young boy's comic book, in which a picture of the medallion is printed. This cut makes it appear as though they still have the medallion, and were able to get the complete spell from it.
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