The 'Single Ladies' musician released a statement to the media on Monday evening confirming that the decision was reached amicably.
She said: "I've only parted ways with my father on a business level. 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 [my father] and my mother manage and own their own businesses. They were hardworking entrepreneurs and I will continue to follow in their footsteps."
The entertainer, who will headline this year's Glastonbury Festival in June, has been managed by her father since she was a teenager.
Mathew Knowles said: "The decision for Beyoncé and Music World Entertainment to part was mutual. We did great things together, and I know that she will continue to conquer new territories in music and entertainment.
"Business is business and family is family. I love my daughter and am very proud of who she is and all that she has achieved. I look forward to her continued great success."
Last summer, reports claiming that the relationship between father and daughter had become strained were quashed by representatives for Beyoncé.