Filming for Transformers: The Last Knight, which stars Mark Walberg and Anthony Hopkins, will take place in Radcliffe Square until 23:00 on Sunday.
Scenes were also reportedly shot at Blenheim Palace, which has previously provided a backdrop for the BFG and James Bond film Spectre, on Wednesday.
The county council said driving scenes would briefly disrupt city traffic.
Academy Award-winner Sir Anthony Hopkins said it was a pleasure to be back in the city, 23 years after filming Shadowlands, in which he played CS Lewis.
He said: "I'm very excited about it, I'm very, very pleased."
It said Turl Street, High Street and Catte Street would be affected and on Sunday Broad Street, Catte Street, Holywell Street, New College Lane and part of Parks Road will be closed.
It has been suggested the fifth outing of the franchise about giant battling robots has a connection to the legend of King Arthur.
The film is due to be released in cinemas next June. Scenes have already been filmed on the Isle of Skye and also at Alnwick Castle in Northumberland.
It is produced by Paramount Pictures and directed by Michael Bay.
Scenes from the upcoming fifth film in the blockbuster Transformers series are being shot in Oxford.