[6] At age 19 he met Guillermo del Toro at the Sitges Film Festival presenting Cronos (1993) and Bayona recognized him as a mentor there.

[6][8] Since then, he has become the principal director of the group Camela and was commissioned to illustrate the piece "Cómo repartimos los amigos", in which the duo Ella Baila Sola bid farewell to their audience.

[10][12] In October of that same year, Variety announced that Universal Studios had signed a contract with Bayona to adapt the film Hater by David Moody, written by Glen Mazzara and produced by Guillermo del Toro.

On 11 September 2016, Keane released a music video for an exclusive new song, "Tear Up This Town", written and recorded for the fantasy drama film A Monster Calls, directed by Bayona.

[16] Bayona was responsible for directing the first two episodes of the Penny Dreadful series, created by John Logan and originally released on Showtime.

In 2014, Bayona began shooting the film A Monster Calls, an adaptation of the novel by Patrick Ness, starring Lewis MacDougall, Felicity Jones, and Liam Neeson.

The film, which was released in 2016, tells the story of a young boy (MacDougall) who cares for his mother (Jones), ill with cancer, while befriending a monster (Neeson).

[17] In 2018, Bayona next directed the science fiction sequel Jurassic World: Fallen Kingdom, starring Chris Pratt, Bryce Dallas Howard, Justice Smith, Rafe Spall, Toby Jones and James Cromwell.

In November 2021, it was announced Bayona would direct the disaster drama Society of the Snow for Netflix, based on the true story of Uruguayan Air Force Flight 571, which crashed into the Andes in October 1972.

[21][22] Back in October 2008, Variety announced that Universal Studios had signed Bayona to direct Hater, an adaptation of British author David Moody's thriller novel about an epidemic of violence caused by regular people.

[15][23] In November 2022, at the Seville European Film Festival, Bayona announced that he was working together with Agustín Díaz Yanes in the adaptation of Manuel Chaves Nogales' book A sangre y fuego.