The book starts out with a girl with magic eye on a flying ship to catch magic sand only she can see. She has no memory of how she grew up. At the start of the journey a man destroys the ship, but safes her. During the book(s) it is reveled that the man and she herself are basically here to destroy humanity because humanity threatens magic. Instead she decides to destroy all magic herself at the end of the last book.
Edit:
Humanity retreated to safe parts of the world where magic isn’t as strong. I think these parts are mostly cities and used completely by humans. Because the magic found in the wild and the land itself is deadly to humans, they can only traverse it using flying ships. Further they use these ships to gather magic gathered in storms to power their machinery. There is also a part where she travels with the demon boy through the wilderness which is super magical and beautiful.
Nah, it’s not this trilogy. IIRC, His Dark Materials is about a girl and a boy and people’s spirit animals, parallel universes, and smiting god (probably).
It was the magic sand only she can see (dust) that was the big similarity to me.
I would describe it less as “smiting god”, and more as “indirectly rescuing god from the control of the church”. Though even that is a bit simplistic.
The “she destroys magic to save humanity” bit does thematically feel very close to the ending of His Dark Materials.