The cast and creative team have been unveiled at a launch event in Jamaica, with Fleabag creator Phoebe Waller-Bridge confirmed as one of the writers.
The unnamed film, which will be released next April, will be Daniel Craig's fifth and final outing as 007.
Malek won an Oscar for playing singer Freddie Mercury in Bohemian Rhapsody.
What role will Malek play?
The official plot summary mentions "a mysterious villain armed with dangerous new technology".
Details of Malek's character haven't been revealed and he wasn't at the official launch on Thursday, but he sent a video message confirming he will play a villain.
"I'm stuck here in New York in production but I'm very much looking forward to joining the whole cast and crew," said the Egyptian-American actor, who is currently filming TV show Mr Robot.
"I will be making sure Mr Bond does not have an easy ride in this, his 25th outing. See you all soon."
After watching that, Craig joked that he was "scared" about what lay in store for Ian Fleming's suave secret agent.
What do we know about the plot?
Bond will again be called upon to save the world from a shadowy adversary - all in a day's work for 007.
The official plot summary reads: "Bond has left active service and is enjoying a tranquil life in Jamaica. His peace is short-lived when his old friend Felix Leiter from the CIA turns up asking for help.
"The mission to rescue a kidnapped scientist turns out to be far more treacherous than expected, leading Bond onto the trail of a mysterious villain armed with dangerous new technology."
At the launch, producer Barbara Broccoli said Bond's attitudes to women would move with the times. "The Me Too movement has had a huge impact - rightfully, thankfully - on society, and these films should reflect that, as everything we do should," she said.
Craig told BBC News: "Bond has always adapted for the times. But you're dealing with a character who is flawed, who has issues, and I think that's something that's worth still exploring and grappling with.
"Of course, we wouldn't be movie-makers or creative people if we didn't have an eye on what was going on in the outside world."
Who else is in the cast?
Lea Seydoux appeared with Daniel Craig in 2015's Spectre
It was also confirmed that Ralph Fiennes and Ben Whishaw will return as M and Q respectively, with Naomie Harris coming back as Moneypenny and Rory Kinnear again playing MI6 chief of staff Bill Tanner.
Lea Seydoux is reprising her Madeleine Swann character from 2015's Spectre, while Jeffrey Wright is returning as ex-CIA agent Felix Leiter.
As well as Malek, new cast members include:
English actress Lashana Lynch played Maria Rambeau, the best friend of Brie Larson's Carol Danvers in Captain Marvel, and starred as Rosaline Capulet in ABC's Romeo and Juliet "sequel" Still Star-Crossed.
Billy Magnussen, a US actor, has had roles in Black Mirror, Game Night and Bond 25 director Cary Joji Fukunaga's Netflix drama Maniac.
Cuban rising star Ana de Armas was Joi in Blade Runner 2049 and will be seen opposite Daniel Craig in another film, Knives Out, in November.
This is the first major film for French newcomer Dali Benssalah, who studied economics and trained as a Thai boxer before turning to acting.
Swedish-Danish actor David Dencik is best known for roles in Tinker, Tailor, Soldier, Spy and Top of the Lake: China Girl.
Who is making the film?
Writer and actress Waller-Bridge, who was also behind the first series of Killing Eve, is just the second female writer in Bond history - after Johanna Harwood, who worked on Dr No and From Russia With Love.
Barbara Broccoli said: "Daniel [Craig] suggested Phoebe, who we all love, so we leapt at the opportunity and she's been amazing, doing great work."
The other co-writers on Bond 25 are seasoned Bond scribes Neal Purvis and Robert Wade along with Scott Z Burns, whose credits include 2007's The Bourne Ultimatum.
The film is being directed by Cary Joji Fukunaga, whose credits include the first series of HBO's True Detective and Netflix's Maniac.
Fukunaga said: "Daniel is my favourite Bond and I want to make sure this run of films, which have been fantastic, have a really great next chapter and keep upping the ante so whoever is next has a harder job."
Fukunaga came on board last year after Danny Boyle left the project over unspecified "creative differences".
There are also changes elsewhere behind the camera. Cinematographer Linus Sandgren, who won an Oscar for Hollywood musical La La Land, comes in as director of photography, while editor Tom Cross won an Oscar for Whiplash.