67 year old Tony Overheu said he was protesting against same-sex marriage and accused Qantas, an Australian airline, of "corporate bullying aimed at social engineering"
The incident happened on Tuesday as chief executive Alan Joyce gave a speech to 500 people in a Perth hotel. Joyce was on stage when Overheu approached from behind, squashed the pie in his face and then walked away.
The former-sheep farmer has also been charged with trespassing, giving police a false name and damage.
Joyce, who is gay, said he will continue to be vocal on social issues despite the incident.
He told reporters in Perth: "Qantas has always spoken up on gender issues, on LGBTI issues, on Indigenous issues and we will continue to do so and no attempt at bullying us into suppressing our voice will work."
Overheu is scheduled to appear in a Perth court next month.