Naldini trained with Pontormo, starting at the very young age of 12 in 1549. In stylistic terms, Naldini owed a lot to his master, even if in the last years of Pontormo’s life their relationship showed signs of deterioration. A few years after Pontormo's death, Naldini spent some time in Rome, after which he returned to Florence. With the exception of a few other short trips away, he stayed there for the rest of his life.
Naldini had various patrons in Tuscany, but he was mainly active for the Medici (particularly for Francesco). He collaborated with Giorgio Vasari in various projects, including the works for the Palazzo Vecchio and the decorations for the funeral of Michelangelo in 1564.
In 1563 Naldini helped to found the Accademia del Disegno – the first drawing academy in Europe – in which he remained active for life. During his last years he was one of the most esteemed painters of religious subjects in Florence.
Naldini created a particular Mannerist style that borrowed from many sources: not only from Pontormo and Vasari, but also from their teacher, Andrea del Sarto. He also showed interest in the work of Raphael and his pupils, such as Polidoro da Caravaggio.