The Derry man missed the cut at 4 over par at the PGA Catalunya Resort in Spain and will play no further part in the final two days.
McGeady's best score was on Monday when he hit a 2 under 70 at the Stadium Course to bring him back to 2 over which still had him in the projected cut zone.
His tournament ended on Tuesday with a 2 over 72 which left him 11 shots of the qualifying target.
The top-25 and ties will secure a playing card for next season when play ends on Thursday.
Kevin Phelan at 6 under and tied for 26th place is the best of the Irish players in the field.