"I've loved every minute of my time on EastEnders," said Berridge, "but felt it the right time to move on to new challenges."
Her decision comes amid severe criticism of the soap's direction and a slump in ratings. In May, the BBC's continuing drama chief Mal Young was forced to issue a statement in support of Berridge, saying that she'd stay despite previous calls for her resignation.
Today, Young said: "This must be the toughest programme-making role on British TV. Louise has done a superb job, overseeing some of the most talked about telly moments of the last three years. It's a relentless job, both as manager and lead creative of over 200 hours of prime time drama, in a very public spotlight.
"There are not many people talented or resilient enough to handle this job, and Louise has proved herself one of the few. Without Louise, there'd be no Alfie Moon, no Dennis Watts.
"At a time of all channels losing audience share, she has helped EastEnders keep its share stable year on year. We're sorry to see her leave her current position, but pleased that she's staying on in BBC drama, as she will now be involved in a major new drama project."
Holby City executive producer Kathleen Hutchison will take over Berridge's position at the soap.