He was more distinguished in architecture than in sculpture. He designed many buildings in Rome, which included work at the Villa Giulia complex (in collaboration with Vignola and Vasari), also at Lucca and Florence. His work at the completion of Pitti Palace, commissioned by Eleonora of Toledo, wife of Cosimo I, is one of his most celebrated achievements (1558-1570), respecting the original style of Filippo Brunelleschi.
He was also employed in 1569 to build the beautiful bridge over the Arno, known as Ponte Santa Trinita and one of his most celebrated works. The three arches are elliptic, and though very light and elegant, have resisted the fury of the river, which has swept away several other bridges at different times. It was destroyed in 1944, during World War II, and rebuilt in 1957.
Another of his most important works was the marble and bronze fountain of Neptune for the Piazza della Signoria. The assignment was originally given to the ageing Bartolommeo Bandinelli. On his death, Ammanati won the competition for the continuing of this assignment over other famous sculptors, such as Benvenuto Cellini and Vincenzo Danti. He worked between 1563 and 1565 on the original block of marble (chosen by Bandinelli), together with his assistants, among which Giambologna. He took Grand Duke Cosimo I as model for Neptune's face. When the work on the ungainly sea god was finished, Michelangelo scoffed at Ammanati that he had ruined a beautiful piece of marble: "Ammanati, Ammanato, che bell' marmo hai rovinato!" Ammanati continued working on this fountain for another ten years, adding, in a mannerist style, around the perimeter suave bronze reclining river gods, laughing satyrs and marble sea horses emerging from the water. The whole gives nevertheless a coherent impression. The fountain served as an example for future fountain-makers.
Other famous sculptures by Ammanati include:
In 1550 Ammanati married Laura Battiferri, an elegant poet and an accomplished woman. Later in his life he had a religious crisis, influenced by Counter-Reformation piety, which resulted in condemning his own works depicting nudity, and he left all his possessions to the Jesuits.
He died in Florence in 1592.