The lengthy trial and malicious reaction from much of the Australia public took a toll on the pair, with their marriage understandably feeling the strain.
In 1991, the couple’s relationship crumbled beyond repair and Michael and Lindy divorced. While they both later insisted Azaria's death wasn’t the reason behind their split, the incident and the ensuing court case and media attention no doubt added to the tension.
After Michael’s death from leukemia in January 2017, news.com.au published previously unreleased emails shining a new light on what went wrong.
Michael wrote that he “always maintained that (Lindy and I) had the ingredients of a good marriage, we had beautiful children, and it could have remained a good marriage ... but we couldn’t quite get there”.
He added: “I remain very saddened by this, despite having had to move on.”
Acknowledging the case had an impact on their relationship, he refused to blame his daughter’s death as the cause behind their split.
“The estrangement has nothing to do with Azaria’s death, but certainly the legal attacks on us following was terrible to both personas and our social self worth,” Michael wrote.
“Nevertheless, the way we approached her death was quite different. Lindy was very emotional, behind the scenes and I was trying to hold it together."
Meanwhile, prior to Michael’s death, Lindy gave her own rare insight into the collapse of the deeply religious couple's seemingly rock solid union, upon her release from prison.
At the National Christian Family Conference in Sydney in 2016, Lindy revealed Michael is the man she had most difficulty forgiving - even more so than members of the public, media and judicial system who helped push her into a wrongful conviction and unjust prison sentence.
The mum of three surviving children, Aidan, 46, Reagan, 44, and Kahlia, 37, declined to go into any further details about her feelings for her ex, adding simply, "that's private".
Lindy previously stated that her marriage did not collapse as a direct result of their family tragedy and the trauma that followed, writing in her autobiography, Through My Eyes: “Many thought my marriage break-up was due to the case and the additional pressures of prison and the press, but it was not.”
Adding more insight into Lindy and Michael's relationship, former journalist and the Chamberlain’s longtime friend Malcolm Brown previously told WHO that their baby’s death drove a wedge between them.
“Lindy was in jail for more than three years. Mike was stuck with the two boys and Kahlia with foster parents, so there were difficulties that arose between them then.”
He added, “When Lindy got out of jail she published a book in 1990 and you could see then she was critical of Michael, accusing him amongst other things of saying that she was too fat. In fact she was pregnant with Kahlia during the trial and he was accusing her of being overweight.”
That accusation, said Brown, “really was very unfair to Lindy, so there were differences between them that were exacerbated by the trauma they went through.”
While Lindy may continue to keep the cards close to her chest as to what really happened between her and Michael behind the scenes all those years ago, she is sharing more details of her ordeal in a new documentary.
Lindy Chamberlain: The True Story, which is set to air Sunday September 27 and Monday, September 28 at 7.30pm on Network Ten, will share never-heard-before details of the case that captured the nation’s attention for so many decades.