The airline also aborted a planned investment in 28 extra weekly flights, which it said would have created a further 400 jobs, blaming what it called the airport's insistence on high landing charges.
The news came only a week after Ryanair announced 1,000 jobs would be created by its opening a new base at Leeds Bradford International Airport.
Only Dublin will remain from the ten destinations at present served from Manchester. Other flights will be rerouted to East Midlands, Leeds Bradford and Liverpool.
The airline said it "continues to lower fares to encourage travel, but with passengers paying lower fares airports must lower their charges".
A spokeswoman for the airport, which is owned by greater Manchester's 10 borough councils, said: "We don't believe that charges as low as £3 per passenger are unreasonable. Clearly, Ryanair do and that's regrettable.
"We've consistently cut our charges for the last 15 years even when faced with increased costs such as security."