Mathieu Roy was charged last Friday in the case of the first victim, who was allegedly assaulted while she was 11 and became pregnant.
Authorities say the new victim is girl under the age of 16.
The new charges come as the 32-year-old man was due back in court Monday for a bail hearing after spending the weekend behind bars.
He now faces two additional charges of sexual assault and sexual touching.
Roy's case has been put off until June 22, when he will return before a judge in Trois-Rivieries, Que., halfway between Montreal and Quebec City.
A bail hearing may be set then.