All flights in and out of the airport will be handled at Terminal One "for the foreseeable future."
The move to concentrate all operations in one terminal comes after England was put into a second lockdown on Thursday for the next four weeks.
The airport closed Terminal Two in September due to falling business. Now Terminal Three will follow be closing too.
Airport bosses say they expect a "significant decrease" in customers over the coming weeks, with the Government advising against all but essential travel.
A spokesman said: "In response to a ban on international travel that forms part of the Government’s current lockdown measures, Manchester Airport is preparing for a significant decrease in customers over the coming weeks.
"With this in mind, and to ensure the best experience for those still flying, the northern hub has taken the decision to operate all flights from Terminal One only from Wednesday 11 November, until further notice.
"From this date, all passengers will depart and arrive from this terminal and should not use Terminals Two and Three. Passengers returning to Manchester after this date whose vehicles are parked in the Terminal Three multi storey car park will be contacted to advise them of this change."
Only essential shops - Pret, Greggs, Boots, Spar (landside); Pret, Boots, WHSmith (airside) - will remain open at the airport
"The UK Government continues to advise against all but essential foreign travel and ignoring this guidance may invalidate travellers’ insurance policies," added the airport spokesman.
"As a result of the lockdown, we expect that a number of airlines will scale back or cancel services during this period. Refunds for cancelled flights are subject to the policy of the airline.
"Passengers are advised to contact their airline if they have any queries regarding service availability. They are also encouraged to thoroughly read all guidance relating to coronavirus from both the UK government and the authorities in their destination before travelling."
Karen Smart, Managing Director at Manchester Airport, said: “The coronavirus pandemic poses an unprecedented challenge to our airport and to our wider industry, but we are determined to provide passengers with the best possible service in the circumstances, ensuring both their safety and comfort.
“When it became clear that England would enter a second national lockdown, we moved quickly to put an appropriate plan of action in place, which will safeguard the continued operation of our airport during these uncertain times. This includes closing Terminal Three from Wednesday 11 November until further notice.
“Changing our operation like this is not straightforward and I would like to thank our dedicated teams for their hard work in preparing for this scenario. We will keep this decision under constant review and communicate any further changes to our customers.
“I would encourage all passengers who will be travelling through Manchester Airport this month to ensure that they are familiar with all of the guidance in place, both from the UK Government and at their destination."
The Government guidance on foreign travel says that if you live in England, you cannot travel overseas or within the UK between Thursday November 5 and Wednesday December 2 unless for work, education or other legally permitted reasons. And you should look to reduce the number of journeys you make.
For those planning to travel into England, you should check the current travel corridor list to see whether you need to isolate for 14 days.
Parking at both the Terminal One and Terminal Three Multi-Storey Car Parks remains open. The airport's Drop & Go service will be put on hold from Wednesday.
Guidance for those picking up/dropping off passengers is: "In order to best enable social distancing and to avoid crowding, people collecting passengers are asked to wait for them in their cars, rather than coming into the terminal to greet them.
"The free drop-off point, next to the JetParks 1 car park, will remain available to use."