The restaurateur, played by Meryl Fernandes, makes her departure in early June as her ongoing problems with husband Tamwar (Himesh Patel) come to a head.
Afia and Tamwar have endured tough times in the aftermath of the Masood family's ordeal with Yusef Khan and the horrifying B&B fire at Christmas.
An EastEnders spokesperson today (May 23) told Digital Spy: "Meryl Fernandes recently finished filming her final scenes at EastEnders, which will be on screen next month."
A show insider added: "Since the traumatic events of the fire, things have not been the same in Tamwar and Afia's relationship. As their issues worsen, they are forced to decide whether their marriage is worth fighting for or whether they have grown apart."
Afia made her first EastEnders appearance in December 2009 and became a full-time character from late 2010.