From 1540, he led the rebuilding of the Basilica of the Santissima Annunziata Maggiore, along with Giovanni Benincasa. The present church however was rebuilt after a fire destroyed Manlio's building in the 18th century. As a result of this, the viceroy of Naples, Pedro Álvarez de Toledo asked Manlio and Benincasa to design a long road connecting the Royal Palace of Naples to one of the city gates. This is now the via Toledo. The pair also redesigned the Castel Capuano, transforming it from a military building into the new Palace of Justice.