The low-cost airline is cutting routes to the French capital and Faro in Portugal from its winter schedule.
The flights will stop running from the airline's Ayrshire hub from November 6 and the company hinted that there could be more cuts next year.
A spokeswoman for Ryanair said it was reviewing all routes for the summer 2014 schedule.
The airline currently operates four flights each week from Prestwick to Paris Beauvais, some 85km north of Paris and five to Faro.
Ryanair said it would be increasing capacity on Prestwick to Dublin routes this winter.
Meanwhile, all flights from Prestwick to Faro are cancelled until March 29.
However some passengers who had booked flights to Portugal appeared to be unaware of the changes.
One posted on the Ryanair site: "I have two Christmas flights booked from Prestwick to Faro return.
"We looked to book someone else on the same flight but the flight appeared to be full. Does anyone know if these flights have been cancelled?"
A spokeswoman for Ryanair said: "Our Faro and Paris Beauvais flights will not operate this winter from Prestwick.
"However, we will operate 42 weekly frequencies, a reduction of just three from the previous winter, with increased capacity on our Prestwick to Dublin route.
"We are continually reviewing our winter schedule as we ground up to 80 aircraft and selectively reduce our winter season capacity, given there is less demand in winter."
The news comes after a French court fined Ryanair more than 8m euros (£6.7m) after ruling that it had broken local employment laws.
The court found Ryanair acted illegally when it employed more than 120 staff on Irish contracts at its former Marseille operating hub between 2007 and 2010.
The low-cost airline said it would appeal against the ruling.