Son of the architect Johannes Weenix, he was born in 1621 in Amsterdam where he was apprenticed to the minor painter J. Micker, to whom he was related.
He subsequently studied under A. Bloemart in Utrecht, and then spent two years in Amsterdam with C. Moeyaert. In 1642/3 he went to Rome where he joined the Schildershera, the colony of Netherlandish artists, and entered the service of Cardinal Pamphilj, later Pope Innocent X, from whom he is said to have adopted his Italianised signature, Gio[vanni] Batt[ist]a Weenix. By June 1647 he was back in Amsterdam, and by 1649 he had settled in Utrecht.
In 1657 he moved to the nearby Huis ter Mey, where he died, aged thirty nine, in 1660/1. Together with Jan Both, J. Asselijn and Karel du Jardin, he was one of the leaders of the second generation of Dutch Italianate painters. His son, Jan Weenix, was also a painter.