The pop superstar and her dad, who had managed her career since she was a teenager, parted ways in 2011.
Mathew Knowles, whose divorce from Beyonce's mother Tina was finalised the same year, insisted the business decision was "mutual" and made so he could concentrate on mentoring gospel singers, but he has now admitted it was tough on him.
In an interview with Britain's The Sun, he says, "Normally I hate to talk about anything personal, but it would be a lie if I did not say it has been difficult.
"It was hard for me to let her go. It was hard for both of us to let each other go, and let's be clear on that. She didn't let me go; we both let each other go.
"This was not a normal ending of a business agreement. This was a dad and a daughter, and it was incredibly painful and it had some difficulties. But I try to always have a positive mind about things and you got to do it the right way."
Tina Knowles filed for divorce from Mathew in 2009, just weeks after he was accused of fathering a lovechild with Alexsandra Wright. A Dna test confirmed Nixon, who was born in February, 2010, is Mathew's son.
Beyonce previously opened up about her business split with her dad in a Tv interview with Oprah Winfrey last month (Feb13).
She said, "It took a while for me and my dad to have an understanding. When I turned 18 and started handling my business more, he went into shock... I’d say no to something, and he’d book it anyway. Then I’d have to do it because I’d look bad (if I didn't). We would fight sometimes, and it took about two years... for him to realise, 'Oh, she is an adult now, and if she doesn’t wanna do something, I can’t make her do it'."