The actress, who plays Michaela McQueen, explained that she is seeking a new challenge.
"I'm leaving Hollyoaks," she told Inside Soap. "I love Michaela and she's absolutely my baby.
"But I'm 23 years old now, and it's time to explore things."
However, Digital Spy has learned that Hollyoaks producers expect Bowes to someday return for a third stint on the teen soap.
Bowes was previously sacked from Hollyoaks in 2010 by former producer Paul Marquess, but was brought back a year later.
Calvin Demba (Scott Sabeka) confirmed his departure last week, while Karen Hassan recently bowed out as Lynsey Nolan.
Bowes joined Hollyoaks in June 2006, since starring in over 270 episodes of the show.
> 'Hollyoaks' Hollie-Jay Bowes: 'I know who killed Lynsey' Get the Inside Soap magazine on your iPhone or iPad