Tomorrow Never Dies is well-known as the film in which the Walther P99 replaces the older PPK as Bond's sidearm. In Saigon, Bond (Pierce Brosnan) picks out the P99 from Wai Lin (Michelle Yeoh)'s hidden armory. Bond states that he has been trying to convince Q to replace his Walther PPK with it. He then uses the gun, with a suppressor attached, through a great deal of the movie's climax aboard the Stealth ship, losing it only when he runs dry during an intense period of gunfire. This is also the gun featured on many posters for the film.

Since then, it has been 007's main sidearm in The World Is Not Enough (1999), Die Another Day (2002) and Casino Royale (2006). For Quantum of Solace (2008), however, the Walther PPK made a return as 007's main sidearm throughout the film. In Skyfall (2012), although primarily armed with a modified PPK/S with a custom grip, Bond appears to be firing a Walther P99 in a production still. This is probably used as an alternative weapon for the Walther PPK.

Although the Walther P99 doesn't feature heavily in the James Bond novel series, Raymond Benson briefly replaced the PPK with the P99 in his novelisation of Tomorrow Never Dies. In the following novels Bond uses both guns: the PPK for undercover work as it is smaller and easier to conceal while he used the P99 for jobs that did not require concealment.