The foundation of the villa of Carmugliano is attributed by tradition to duke Alessandro de Medici after the year 1532. It later passed to the Salviati’s, the Gondi’s and to the Marchese Matteo Botti, the grand duke’s Master of the Chamber. Following the grand duke’s bankruptcy it was confiscated and the deeds were held in the possession of the Medici bank. According to an inventory carried out during that period, all the property was in a very bad condition and the building itself did not appear to be structurally sound.

In 1634 negotiations were begun by Filippo Niccolini, a Florentine nobleman, for the purchase of the holding. On 23rd September 1634 the price was settled at 50.000 scudi and successively a title, already held by Niccolini, was commuted by the grand duke to that of Marcheses di Ponsacco e Carmugliano. Filippo immediately began the impressive works on the villa as recommended by his expert advisors. The general state of the farm was also improved by increasing cultivation, regaining swamp land and planting new vineyards.

The present day aspect of the villa which is due to Filippo and the Florentine architects he hired to carry out the works has inspired changes to be made to other late 1500 Medici villas. It is probable that the walls were strengthened by being ‘lined’ following a report from the surveyors stating that they were too thin. In fact three of the four corner towers were built completely new and the existing one was modified to conform to their shape. The large area in front of the south façade was enclosed by two independent wings consisting of the granary and the stables towards the west and of the farm-buildings towards the east. The foundations of the villa were fortified by thick containing walls. The loggia is similar to the one built by Filippo in 1655 in the internal courtyard of his residence in Florence in Via dei Servi. It was in these years that the splendid chapel in the basilica of Santa Croce was begun.

The private chapel dedicated to St. Philip is situated on the ground floor along the long main corridor which crosses the whole width of the building. On the first floor the vaulted ceiling of the large central hall was frescoed by Angelo Michele Colonna. It was from the year 1640 that the park was planned out and the avenues of cypress trees were created leading to the Church of San Frediano and other parts of the park. Following the death of Filippo in 1666 considerable improvements were carried out on the numerous farm buildings on the estate and the cellars were enlarged whilst at the villa the loggia was closed in. The field to the south was enclosed by a perimeter wall on which marble busts were placed with a central statue of Hercules by Giovanni Bandini (known as Giovanni dall’Opera). All these works came from the famous collection of sculptures at the mansion house in Via dei Servi following its sale. Stone coats of arms were placed at the external corners of each of the towers bearing the arms of the Niccolini family and of the families to which they were joined by matrimony.
Most of these works and modifications took place under the marquisate of Giovanluca (died 1752) and Lorenzo (died 1795). During the following century, another Lorenzo (died 1868) created the English Garden and commissioned a meticulous re-elaboration of the entire estate. In fact the villa gained recognition of being such a prestigious residence that in 1857 the grand duke Leopoldo asked for hospitality to be given to Pope Pio IX during his visit to Tuscany.