In the 1997 James Bond film Tomorrow Never Dies, he had a small role playing a naval sailor onboard "HMS Bedford".

His early roles were usually good-natured bumbling characters like Bernie in Notting Hill (1999) and Mr Rushworth in Mansfield Park (1999).

In Iris (2001), he played the young John Bayley opposite Kate Winslet, with his performance lauded by critics and receiving a BAFTA nomination for Best Supporting Actor.

He played the role of Jerry Westerby in the BBC Radio 4 dramatisation of the John le Carré novel The Honourable Schoolboy, first broadcast in January 2010.

On 18 November 2012, Bonneville appeared on stage at St Martin's Theatre in the West End for a 60th anniversary performance of Agatha Christie's The Mousetrap, the world's longest-running play.

He has appeared in the singing comedic role of Peter the Pillager, the Pirate King, in the ABC fairy tale-themed musical comedy extravaganza series Galavant during its 2015 and 2016 seasons.

In 2017, Bonneville portrayed Lord Mountbatten in director Gurinder Chadha's film Viceroy's House, which depicted the tumult and violence surrounding the Partition of India during the final days of British rule.

Also in 2017, he portrayed the voice of Merlin in the movie based on the children's TV series Thomas & Friends, Journey Beyond Sodor.

Also that year, he narrated the documentary A Return to Grace: Luther's Life and Legacy and it was announced that Bonneville would play Roald Dahl in an upcoming biopic about the author.

In 2019, Bonneville portrayed C. S. Lewis at the Chichester Festival Theatre's production of Shadowlands,[17] along with actors Liz White and Andrew Havill.

[25] Bonneville is also a patron of the London children's charities Go Live Theatre Projects[26] and Scene & Heard, as well as an ambassador for WaterAid.