For the first time, she entered Portsmouth with F-35B Lightning II jets on her flight deck.
HMS Queen Elizabeth - the joint biggest and most powerful warship ever built for the Navy - had been expected to complete her pre-deployment preparations at anchor in the Solent following Exercise Strike Warrior.
However, poor weather forecasts mean this will now be done alongside at the naval base.
Personnel will remain on board the carrier as part of COVID-19 measures.
Other ships deploying as part of the Carrier Strike Group will complete their pre-deployment preparations at Devonport Naval Base in Plymouth and Clyde in Faslane.
The Carrier Strike Group is expected to set sail as planned for the deployment which is the Navy's biggest in more than a decade.
It will see the ships sail more than 26,000 nautical miles, travelling through the Atlantic, Mediterranean Sea, Suez Canal, Arabian Sea, Indian Ocean, South China Sea and more.
Over 28 weeks, the group will also visit India, Japan, South Korea, Singapore and the wider region.
What ships and aircraft are also deploying?
Eight ships are joining HMS Queen Elizabeth, the nation's flagship, on the Carrier Strike Group 21 deployment.
A Royal Navy Astute-class submarine will also be deployed in support.
Watch: What makes up a Carrier Strike Group?
The task group will be supported by two ships from the Royal Fleet Auxiliary - RFA Tidespring and RFA Fort Victoria - which will help replenish the other vessels with supplies, equipment, fuel and food.
Aircraft from several squadrons will also help make up the Carrier Strike Group.
Wildcat helicopters will be flown by 815 Naval Air Squadron, and Merlins will also be operated by 820 Naval Air Squadron and 845 Naval Air Squadron.
In total, 3,700 personnel will be a part of the Carrier Strike Group, including personnel from 42 Commando, Royal Marines.