Where applicable, the names of these deleted scenes have been taken from the Blu-ray release of Alien: Covenant.
The opening scene with Peter Weyland and the newly activated David was originally considerably longer, with more dialogue between the two. This can be seen on the Blu-ray and most of the additional lines appear in the film's novelization.
Walter in Greenhouse
While Walter is checking the Covenant before the neutrino burst hits the ship, he was originally seen tending to the plants in the ship's hydroponics bay. He whistles to the plants, leading MU-TH-UR to question him about the myth that playing music to plant life encourages it to grow. This scene appears on the Blu-ray and in the novel.
Oram and Daniels (Extended)
After the crew meets on the bridge to assess the damage to the Covenant, Oram takes Daniels to one side and tells her how much he respected Branson, before telling her to take some time off to "cry it out", a suggestion she rejects. This sequence is on the Blu-ray and also in the film' novelization.
Walter Visits Daniels
Another deleted scene that would have followed on from the above addition shows Daniels in her quarters. Walter visits her and offers her some cannabis, which he has grown in hydroponics, telling her it will help her relax. This scene can be found on the Blu-ray and in the novel.
Daniels Bedroom Flashback
The film originally featured an additional Earth-set scene in which Daniels remembers being with Branson in their New York apartment, snow falling outside the window. During the flashback, the couple would have discussed their future on Origae-6, including their desire to construct a log cabin on a lake there, mentioned several times in the finished film. This scene is featured on the Blu-ray. While it also appears in the novelization, it is moved to the start of the film, in the form of a dream Daniels is having whilst in hypersleep.
Jacob's Funeral (Extended)
Before Branson's funeral, Oram sits alone on the bridge, playing with a set of metal worry beads and looking at a photo of an old man (presumably his father). Elsewhere on the ship, Daniels invites Walter to attend the imminent funeral; when Walter asks why, Daniels points out that she is now alone on a ship full of couples, something she suspects Walter may know a thing or two about. This can be seen on the Blu-ray.
Crossing the Plaza (Extended)
The scene where David leads the survivors into the ruined Engineer city was originally longer. As they walk through the scores of dead Engineers, the survivors pass a vast opening in the ground. Lopé lights a flare and tosses it into the chasm, and it is revealed to be an Engineer hangar similar to the one seen in Prometheus, filled with vessels. This sequence appears on the Blu-ray.
Daniels Thanks Walter
Inside the citadel, Daniels thanks Walter for saving her from the Neomorph, before pointing out that there is much about David's presence that doesn't make sense. Walter promises to discuss it with his counterpart. This scene is on the Blu-ray and appears in the novelization.
Just before she is killed, Rosenthal originally said a short prayer in Hebrew. As she does, the Neomoprh is seen sneaking up on her through a dark passageway. This can be found on the Blu-ray.
Walter Reports Back
Another dialogue scene cut while the survivors hole up inside the citadel has Walter returning to Daniels, Oram and Lopé to report on his discussions with David. He says that he is concerned for David's mental state and the fact he has obviously not been receiving proper maintenance whilst alone on Planet 4. Afterwards, the group notices Rosenthal is missing and Oram goes to look for her. This scene is on the Blu-ray and is also included in the novelization.
Stairs to Eggroom (Extended)
On the way down to David's Egg chamber, Oram originally balked at the smell. David subsequently hands him some ointment to rub under his nose and mask the stench. This additional dialogue is on the Blu-ray and in the novel.
Four Meters Above You
In the film's "She Won't Go Quietly" trailer, the final scene shows Daniels question where the Xenomorph is aboard the Covenant, to which MU-TH-UR responds, 'Four meters above you', before the Xenomorph appears to attack from above. This footage is absent from the final film.