The Manchester City star, 33, has been involved in a number of off-pitch scandals during his long-term relationship with Annie, 30.
She repeatedly forgave her partner before the couple, who have three kids together, tied the knot in 2021.
Kyle is no longer living at the family’s £2.5million property in Cheshire.
In a post on her Instagram story Annie Kilner said: “I am posting this in response to growing recent media enquiries about my marriage to Kyle and in an effort to protect my family against the intensity of the media spotlight.
“Sadly, after many years of marriage and three wonderful children together, I have decided to take some time away from Kyle.
“I do not wish to comment on the position any further. For now, I ask that the privacy of myself and our 3 young children is respected during this difficult time.”
It comes after a number of scandals in which the footballer had repeated romps in a Bentley with Ex On The Beach star Laura Brown in 2019.
After rekindling their romance, it was then revealed in March 2020 that model Lauryn Goodman was having Kyle’s baby.
Annie again forgave Kyle, but he found himself embroiled in further controversy when he was then caught breaching Covid lockdown rules by having an orgy with two hookers.
And last year, Kyle attended a voluntary interview with police after he snogged and flashed a woman in a Manchester bar.