The "Rise Up" singer's former manager, 61, was engaged to 48-year-old Avery, currently a realtor, for a year and a half.
Knowles, head of Music World Entertainment, stopped managing his daughter's career in March 2011. In a statement to Us Weekly at the time, Jay-Z's wife, 31, said there was no hard feelings based on her decision.
"I've only parted ways with my father on a business level," Beyonce said. "He is my father for life and I love my dad dearly. I am grateful for everything he has taught me. I grew up watching both he and my mother [Tina Knowles] manage and own their own businesses. They were hard-working entrepreneurs and I will continue to follow in their footsteps."
Knowles' divorced Beyonce's mother, Tina, in 2011 after 31 years of marriage.
This article originally appeared on Usmagazine.com: Beyonce's Dad Remarries: Mathew Knowles Marries Gena Charmaine Avery