Dame Lynne first joined the Met as a constable in 1989 before taking in an array of high-profile roles, including as the first female Chief Constable of Surrey Police and Director General of the NCA.
Mayor of London, Sir Sadiq Khan, who will help appoint the next Deputy Commissioner alongside the force and the Home Office, said he wished Dame Lynne “happy retirement”.
Dame Lynne, who began her career as a Met constable in Catford before rising through the ranks to take on high-profile jobs such as Director General of the National Crime Agency, will retire in late May.
The force on Tuesday hailed Dame Lynne’s efforts as helping the Met leave special measures in January, as well as making “major progress” towards reform.
The second most senior officer in the Met Police, Dame Lynne Owens, will retire after more than 35 years in policing.