Earlier this month, it was confirmed that the star would be departing Albert Square as Tom 'Rocky' Cotton after two years on the soap.
Addressing Conley leaving, Bowden told The Mirror: "I love Brian Conley, I am very, very sad. With what we do you see it happen all the time, people come and people go and it's either down to personal circumstance or people wanting to try other things.
"Brian is an incredibly successful man, and he will go on to smash whatever he does next," the star continued. "It's gonna be a huge loss to us, I'm sure he's doing the right thing by him and I wish him all the best."
Following the initial reports of his exit, Conley confirmed that he indeed would be leaving, while also denying reports that he had fallen out with show bosses.
"You may have heard reports that I'm leaving EastEnders. It was a tough decision but it is true, I am going and I made it for many reasons, that decision," he said. "It is tough because they're such a wonderful crowd, in front of the cameras and behind the cameras and I've loved my three years there.
"So that's the truth in the reports. There's other parts of reports saying that I clashed with TV bosses and the crew. I didn't clash with anyone. I didn't have a rant. But they'll probably report on this now that I'm ranting about ranting! But I'm not ranting!
"I have gone with their blessings at the Beeb and I'm excited about the future and where it's going to go. And I'm also excited about Rocky's exit because I know it's good. So I'm sending you much love – all EastEnders fans."
The soap itself said there was "absolutely no truth in any claims of a feud with bosses and the show fully supports Brian in his decision to leave which was made some time ago".
"We wish him the best of luck for the future as we continue to work towards his exit storyline which has been in the works for some time," they added.
EastEnders airs on Mondays - Thursdays at 7.30pm on BBC One. The show also streams on BBC iPlayer.
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