The Spain Under-21 international, 20, is set to sign a five-year deal with the La Liga side after rejecting a late offer from the Gunners.
Merida arrived at the Emirates from Barcelona in 2006 but has yet to make his full league debut and spent 2008 on loan at Real Sociadad.
His agent Joseba Diaz said: "Fran's decision is based purely on sporting questions and not money."