2000–2010: Being Julia, Elizabeth I and roles in blockbusters
To mark the 100th anniversary of Noël Coward's birth, Irons sang a selection of his songs at the 1999 Last Night of the Proms held at the Royal Albert Hall in London, ending with "London Pride", a patriotic song written in the spring of 1941 during the Blitz. In 2003, Irons played Fredrik Egerman in a New York revival of Stephen Sondheim's A Little Night Music, and two years later appeared as King Arthur in Lerner and Loewe's Camelot at the Hollywood Bowl. He performed the Bob Dylan song "Make You Feel My Love" on the 2006 charity album Unexpected Dreams – Songs From the Stars. Other roles include the wicked wizard Profion in the film Dungeons and Dragons (2000) and Rupert Gould in Longitude (2000). He played the Über-Morlock in the film The Time Machine (2002). In 2004, Irons played the title character in The Merchant of Venice. In 2005, he appeared in the films Casanova opposite Heath Ledger, and Ridley Scott's Kingdom of Heaven. He reunited with his The Man in the Iron Mask co-star John Malkovich in Eragon (2006), though they didn't have any scenes together this time. In 2004 Irons played Severus Snape in the BBC's Comic Relief's Harry Potter parody, "Harry Potter and the Secret Chamberpot of Azerbaijan".
In 2004, he starred in István Szabó's Being Julia opposite Annette Bening, receiving a Satellite Award nomination for his performance. In 2005, Irons portrayed Robert Dudley, 1st Earl of Leicester in the Channel 4-HBO mini-series, Elizabeth I, in which he starred opposite Helen Mirren (Queen Elizabeth I). Rupert Smith of The Guardian praised their on-screen chemistry, writing, "Mirren and Irons are a screen marriage made in heaven, and when they let rip with the thwarted passion all might have been well." Irons won both a Primetime Emmy Award for Outstanding Supporting Actor in a Limited Series or Movie and a Golden Globe Award for Best Supporting Actor – Series, Miniseries or Television Film for his performance.
A year later, he participated in the third series of the BBC documentary series Who Do You Think You Are? In 2008, he played Lord Havelock Vetinari in Terry Pratchett's The Colour of Magic, an adaptation for Sky One. In 2006, Irons appeared with Laura Dern in David Lynch's Inland Empire. After an absence from the London stage for 18 years, in 2006 he co-starred with Patrick Malahide in Christopher Hampton's stage adaptation of Sándor Márai's novel Embers at the Duke of York's Theatre. He made his National Theatre debut playing former British Prime Minister Harold Macmillan (1957–1963) in Never So Good, a new play by Howard Brenton which opened at the Lyttelton on 19 March 2008. In 2009, Irons appeared on Broadway opposite Joan Allen in the play Impressionism. The play ran through 10 May 2009 at the Gerald Schoenfeld Theater.
In 2008, Irons co-starred with Ed Harris and Viggo Mortensen in the western drama Appaloosa, directed by Harris. On 6 November 2008, TV Guide reported Irons would star as photographer Alfred Stieglitz with Joan Allen as painter Georgia O'Keeffe, in a Lifetime Television biopic, Georgia O'Keeffe (2009). For his performance, he was nominated for the Golden Globe Award for Best Actor – Miniseries or Television Film and the Screen Actors Guild Award for Outstanding Actor in a Miniseries or Television Movie. In 2008, two researchers, a linguist and a sound engineer, found "the perfect [male] voice" to be a combination of Irons's and Alan Rickman's voices based on a sample of 50 voices. Coincidentally, the two actors played brothers in the Die Hard series of films. Speaking at 200 words per minute and pausing for 1.2 seconds between sentences, Irons came very close to the ideal voice model, with the linguist Andrew Linn explaining why his "deep gravelly tones" inspired trust in listeners.
In 2009, Irons appeared on the Touchstone album Wintercoast, recording a narrative introduction to the album. Recording took place in New York City in February 2009 during rehearsals for his Broadway play Impressionism. As German villain Simon Gruber his recital of the English riddle "As I was going to St Ives" (from Die Hard with a Vengeance) appears in the 2014 book The Art of Communicating Eloquently. In 2017, he recited the spoken sections, most notably "Late Lament", for The Moody Blues' 50th Anniversary Tour of "Days Of Future Passed", and also appears on the video presentation. Irons also appeared in the documentary for Irish television channel TG4, Faoi Lán Cheoil, in which he is seen taking fiddle lessons from Caoimhín Ó Raghallaigh.