Many alterations and additions were proposed and made over the next two centuries, including plans by Gherardo Mechini, Paolo Guidotti, Ranieri Gherardi, Torpè Donati, Alessandro Gherardesca, Florido Galli, Niccolò Matas, and Pasquale Poccianti.

The final reconstruction in 1859, completed after the suppression of the order, creates the clearer interior systematization of columns we see today.

In the counterfacade are five monochrome paintings of Stories of St Stefano Pope and Martyr, including one celebrating the entrance of Ferdinando I on 31 March 1588.

The Ceiling has six paintings on wood depicting episodes historic events in which the military order was active, including the Granting of uniforms by Cosimo I de' Medici by il Cigoli, the Return of the Fleet from the Battle of Lepanto and Sacking of Prevesa by Jacopo Ligozzi, The embarcation at Livorno of Maria de' Medici by Allori, Victory in the Greek Archipelago and Capture of Bona by l'Empoli, The polychrome pulpit (1627) was completed by Chiarissimo Fancelli.

In the Sacristy is a sculptural group by Foggini of St Stefano and the allegory of Reason and the Trinity (1683), made in occasion of the translation of the body of the saint to this church in 1682.