The former Coronation Street actress is said to have told friends that her four-year relationship is over "for good this time".
The 22-year-old is apparently in the process of moving out of their shared Cheshire home, reports The Sun.
Last week, she tweeted: "New chapter, got to be happy."
A friend of the couple said: "Helen and Scott break up every other week. It is something all of her friends have got used to. But the fact that she's told close pals it's all over is a new step.
"She loves Scott, but thinks breaking free will give her a new lease of life. The fact she is talking so publicly about 'the end' means this could be it for good."
Back in February, Flanagan called the police over fears that a burglar was attempting to get into her house, but it was actually the Manchester City player coming home from a night out.
Initial reports of issues in the couple's relationship emerged in January, before Flanagan stated that she wanted to have children with the footballer.
She said at the time: "No relationship's perfect, but we really love each other and we're really strong. We're complete opposites. He's so laid-back and I'm very sensitive. He says, 'I don't like you reading things [in the papers]'.
"Me and Scott both want a baby... I'm like his stalker. You have to have that kind of love where you'd die for that person. It has to be really intense and passionate and true, crazy love."
Yesterday, Flanagan hinted that she may leave Twitter over criticisms of her online comments.
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