"She loved Ben," a close friend told People. "But there comes a time when you have to say enough is enough and take care of yourself."
Ben and Jen throughout the years:
Ben and Jen through the years
Ben Affleck and Jennifer Garner's split fuels cheating rumors
Actor Ben Affleck and wife, actress Jennifer Garner smile at catcher Doug Mirabelli #28 of the Boston Red Sox as they attend the game against the New York Yankees during the game at Fenway Park on October 1, 2005 in Boston, Massachusetts. (Photo by Jim McIsaac/Getty Images)
Actors and husband and wife, Ben Affleck and Jennifer Garner listen to the national anthem before the Boston Red Sox host the New York Yankees on June 2, 2007 at Fenway Park in Boston, Massachusetts. (Photo by Elsa/Getty Images)
Actress Jennifer Garner (L) and actor/director Ben Affleck, winner of Best Picture for 'Argo', departs the Oscars at Hollywood & Highland Center on February 24, 2013 in Hollywood, California. (Photo by Frazer Harrison/Getty Images)
Jennifer Garner and Ben Affleck attend the Boston Celtics versus the Orlando Magic in Game Seven of the Eastern Conference Semifinals during the 2009 NBA Playoffs at TD Banknorth Garden on May 17, 2009 in Boston, Massachusetts. (Photo by Elsa/Getty Images)
Actor Ben Affleck and actress Jennifer Garner pose during the 16th annual Critics' Choice Movie Awards at the Hollywood Palladium on January 14, 2011 in Los Angeles, California. (Photo by Christopher Polk/Getty Images for VH1)
Actress Jennifer Garner and actor-director Ben Affleck arrive at the Oscars at Hollywood & Highland Center on February 24, 2013 in Hollywood, California. (Photo by Jason Merritt/Getty Images)
Ben Affleck and Jennifer Garner are seen in Brentwood on April 24, 2015 in Los Angeles, California. (Photo by GONZALO/Bauer-Griffin/GC Images)
LOS ANGELES - FEBRUARY 9: Cast members (L to R) Colin Farrell, Michael Clarke Duncan, Jennifer Garner and Ben Affleck pose for photos at the premiere of 'Daredevil' at the Village Theatre on February 9, 2003 in Los Angeles, California. (Photo by Kevin Winter/Getty Images)
(EXCLUSIVE, Premium Rates Apply) Jennifer Garner (on screen) and Ben Affleck *Exclusive* (Photo by Mathew Imaging/FilmMagic)
(EXCLUSIVE, Premium Rates Apply) Jennifer Garner and Ben Affleck *Exclusive Coverage* (Photo by Mathew Imaging/FilmMagic)
Jennifer Garner and Ben Affleck during Ben Affleck and Jennifer Garner on Location for ''Gone Baby Gone'' in Boston, Mass - May 24, 2006 at on location in South Boston, Massachusetts, United States. (Photo by Marc Andrew Deley/FilmMagic)
Actor Ben Affleck and actress Jennifer Garner come off stage at the 24th Annual American Cinematheque Award presentation to Matt Damon at The Beverly Hilton hotel on March 27, 2010 in Beverly Hills, California.
LOS ANGELES, CA - DECEMBER 16: Jennifer Garner and Ben Affleck in Brentwood on December 16, 2012 in Los Angeles, California. (Photo by Bauer-Griffin/GC Images)
Meanwhile, Us Weekly's sources are telling two different stories.
While one "insider" says Affleck did not cheat on the 43-year-old actress, another claims she once kicked him out of their house amid the speculation, only to later reconcile. "She tried to leave him a few times, but he would beg her to stay," a source claims.
"She always fought against the urge to throw her hands up in the air and walk away," another Us insider alleges. "They've been on the brink of splitting up many times before, but it's Jennifer's worst nightmare for their children. Her biggest desire has always been to keep the family together."
According to the magazine, one of Affleck's pals says he's not taking the separation well. "This is just as hard on him and difficult for him. Any divorce is tough on everyone. He is leaning on his mom and close friends."
ET has reached out to Affleck's reps regarding these reports.