The hometown favourite began his maiden title defence at a quick tempo, but was caught by Flores in an even first round.
From then on, though, it was all Bellew as he knocked the American down three times in the second round, with Flores eventually being saved by the bell.
Both fighters came out swinging in the third round, but it took just one more knockdown before the referee called an end to the bout.
It was the first time that Flores has been stopped in his career, and after the bell Bellew made a beeline for long-time rival David Haye at ringside.
The Liverpudlian then called out Haye in his post-match interview, seemingly setting up a future heavyweight bout between the British rivals.