The 51-year-old said he has been "humbled by the love", but was ready to leave Albert square as the Masood family expands.
His character's feisty nieces Iqra and Habiba are set to bring trouble to Walford after being hired by ex-Corrie boss Kate Oates.
In a statement to Digital Spy, Nitin said: "When I was asked to return to EastEnders, it was always with the intention of helping set up new Asian characters that continue the Masood family adventures.
"With Arshad and Mariam at the helm and with the arrival of the feisty sister Iqra and Habiba, I can now venture off to new horizons as an actor.
"I am still deeply attached to Masood and have invested much emotion into making this character memorable.
"I am in awe of how loved he is by audiences and fans of all ages, from all cultures and religions and walks of life. Thank you. I am humbled by the love.
"I will of course miss EastEnders and the wonderful people that work tirelessly to bring audiences dramatic, funny and compelling stories."
Nitin joined EastEnders in 2007, before he left briefly nine years later.
But he couldn't stay awake and was back in late 2017, leaving fans with the hope he could make a return once more.
An EastEnders spokesman said: "Nitin has been a wonderful addition to the cast and we wish him all the very best for the future."
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