The Wonder Woman actress – who stars as Rachel Stone – was seen with a facial injury as she filmed scenes at the popular attraction on Wednesday.
The scenes centred around a former RAF Hercules C-130 transport plane on display outside the museum, which remained open to the public during filming.
It comes after the 37-year-old was joined by her co-star Jamie Dornan, whose role in the film has not yet been revealed, to shoot scenes for Heart Of Stone in London last week.
The film's plot is being kept tightly under wraps while many of the stars' roles have not been revealed. So far, the film is being described only as a spy thriller.
In September last year, Gal was announced to be leading the cast of Heart of Stone playing the role of Rachel Stone. Also joining the cast are Sophie Okonedo, Alia Bhatt and Matthias Schweighöfer, while Tom Harper is directing.
The movie is being developed by Skydance Media, the production company behind projects such as Mission: Impossible: Fallout, The Old Guard and Annihilation. Netflix secured the rights to the movie after a competitive and heated bidding war.
It comes after an A-list cast from BBC's Great Expectations – including the likes of Olivia Colman and Tom Hardy – descended on Shrewsbury earlier this week.
A spokeswoman for RAF Museum said: "I can confirm that Netflix were present filming at the location and Gal Gadot was present."