His return to Valencia, he was appointed as a professor of Hebrew at the University of Valencia in 1563 and two years later he was appointed as a professor of mathematics.
In 1578 he moved to Salamanca where he was a professor of mathematics and astronomy. It was there that he probably taught the theories of Copernicus’ De revolutionibus.
Apart from his University teaching, he pursued various activities related the new technologies of the time as an expert or assessor. These included:
Carrying out a census of the population of Valencia
Elaborating a map of what is now the autonomous region of Valencia.
Intervening in a law suit concerning water rights between the towns of Lliria and Benisanó.
Moving to Murcia to carry out a project commissioned by the king “for water conduction and distribution”. He supervised the work involved in leveling the terrain and determined the precise latitude of Murcia to be 37º57´.
Responding to the call of the city authorities of Salamanca, who requested his services in directing the construction of a conduit to bring spring water to the city.
Muñoz was married to Isabel de Valenzuela and had three daughters and one son, to whom Muñoz’s writings and books were passed down.