One insider confided to Page Six that trouble had been brewing for months.
“She thought he had become too controlling during the pregnancy and she had already allowed him to dictate her appearance and even the way she performed at concerts,” a source, who works closely with the couple, told the publication.
Janet secretly married the 42-year-old Qatari businessman back in 2012, before welcoming their son this year, on January 3.
The singer's brother Jackie recently claimed that the trio were happier than ever.
"Janet had a beautiful baby boy. It's all good," he told Good Morning Britain.
"Everyone's fine. Everyone's great."
But away from glossed-over family spin, there has been speculation that something a little darker has been at play.
Despite their five-year marriage, Janet was said to be upset by her partner's desire to change her.
The New York publication claim that Wissam wanted his wife to tone down her style and the image she projected in her music.
“It drove her crazy and she felt she was losing her fan base.”
However another friend told the Mail On Sunday it was an amicable split.
"Sadly, Janet and Wissam have decided that it wasn't working and to go their separate ways," the pal said.
"They're both busy people but determined to be good parents, even if they're apart. It's amicable and Eissa will stay with his mother, who is basing herself in London."
Wissam was Janet's third husband. She was previously married to singer James DeBarge and dancer Rene Elizondo.
While the 50-year-old had been very private about her relationship, last year she shared her pregnancy news with fans.
"My husband and I are planning our family, so I'm going to have to delay the tour," she explained in a Facebook video message in April, 2016.
"Please, if you can try and understand that it's important that I do this now. I have to rest up, doctor's orders! But I have not forgotten about you. I will continue the tour as soon as I possibly can."
Neither Janet or Wissam have yet to make a comment about the news.