Bayeu was born in Zaragoza and apprenticed there. In 1758 he won a scholarship to study with Antonio González Velázquez at the Academy of San Fernando in Madrid, but was expelled for not attending classes and soon returned home. In 1762 he moved to Madrid where he was taken up by the new court painter, Anton Raphael Mengs.
Bayeu abandoned his Rococo style for Mengs's neoclassical manner. He became an accomplished fresco painter and was much in demand, working on nearly all the principal decorative schemes of the time including the royal palace, the royal residence at Aranjuez, the cloister of Toledo cathedral and several projects in the basilica of El Pilar in Zaragoza. His frescoes are painted in the grand manner, although he retained the brighter palette of his early years for his oil sketches.
He eventually became Director of the Madrid Academy and court painter to the newly crowned Charles IV. By the end of his career Bayeu was the leading painter in the Spanish artistic establishment.