Mr Johnson met with Her Majesty in the drawing room of the private royal residence where the former Tory party leader offered his resignation.
He arrived at Balmoral Castle, Aberdeenshire, with wife Carrie Johnson for his final audience with the monarch.
He was greeted by the Queen’s private Secretary Sir Edward Young and her Equerry Lieutenant Colonel Tom White, and said “good morning” a number of times to the Queen’s aides.
Pages were on hand to open the doors of the chauffeur-driven car which arrived in light rain and stopped at the front door.
It comes after Mr Johnson made his final speech as Prime Minister outside No.10 this morning.
He said: “This is it, folks. Thank you everybody for coming out so early this morning. In only a couple of hours I will be in Balmoral to see Her Majesty the Queen and the torch will finally be passed to a new Conservative leader.
“The baton will be handed over in what has unexpectedly turned out to be a relay race. They changed the rules halfway through, but never mind that now.”
Mr Johnson celebrated "getting Brexit done" and the success of the vaccine rollout in his address.
He said: “Through that lacquered black door, a new prime minister will shortly go to meet a fantastic group of public servants.
“The people who got Brexit done. The people who delivered the fastest vaccine rollout in Europe, and never forget 70 percent of the entire population got a dose within six months – faster than any comparable country.
"That is government for you. That’s this Conservative government.”
Liz Truss will take over from Mr Johnson on Tuesday afternoon, after also making the trip to the Queen's Highlands home.
The monarch has opted not to travel back to London for the customary Buckingham Palace address with the Prime Minister in waiting.
Her Majesty will hold an audience with the new Tory leader, where Ms Truss will be invited to form a government and take over as PM.
Boris Johnson outside No.10 on Tuesday
Stefan Rousseau
Boris Johnson greeted by the Queen's Equerry Lieutenant Colonel Tom White
Andrew Milligan