The 44-year-old director, who most recently worked on blockbuster Jurrasic World: Fallen Kingdom, will also executive produce the series, reported Variety.
“JRR Tolkien created one of the most extraordinary and inspiring stories of all time, and as a lifelong fan it is an honour and a joy to join this amazing team,” Bayona said in a statement.
“I can’t wait to take audiences around the world back to Middle-earth and have them discover the wonders of the Second Age, with a never-before-seen story,” he added.
Recently, Bryan Cogman, who worked as a writer and co-executive producer on Game of Thrones, boarded the project as a series consultant.
He is helping out the writing team of Patrick McKay and JD Payne, who were announced as series developers last year.
Amazon has made a multi-season production commitment to the TV series. It will produce the show in cooperation with the Estate of J R R Tolkien, publishing house HarperCollins, and New Line Cinema, a division of Warner Bros.
However, the series will not be a retelling of Peter Jackson’s Oscar-winning trilogy. It will explore story set before the events in the first LOTR novel, The Fellowship of the Ring.