According to the Metropolitan Police, he oversaw an 18 per cent fall in London crime figures during his tenure.
Announcing the decision, the 58-year-old said: "I am so proud of the remarkable men and women who serve Londoners as police officers and staff and make this such a safe place for people to live, work or visit.
"I want to thank all of them for what they do, and the risks they take each day to protect the public.
"I came into this job determined to fight crime and make the MPS [Metropolitan Police Service] the best, most professional police service. I wish my successor well as they take on this amazing responsibility.
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"It has been a great privilege to be the Met's Commissioner. I have loved my time in the role and I have loved being a police officer.
One of Britain's senior-most police officers had first joined the Met - the UK's largest police force - as Assistant Commissioner in July 2001.
He had been expected to remain in his current role until at least September next year after then Home Secretary Theresa May had extended his contract, which was due to expire this month.
UK home secretary Amber Rudd described Sir Bernard as a "determined crime fighter and an inspirational senior officer".
Mayor of London Sadiq Khan thanked him "for his years of service and dedication to keeping Londoners safe".