Villa Beatrice was named after Saint Beatrice who lived here between 1221 and 1226. On the site of the villa, a small coenobium stood once earlier inhabited by hermits. Beatrice descended from the noble family D'Este, which, before moving to Ferrara, had ruled over the town of Este and over part of Padua territories. She took vows in the small nunnery of Saint Margherita of Salarola, located between Mount Cero and Mount Castello; in 1221 she moved to Mount Gemola and there restored an abandoned convent. Beatrice lived here sharing her strong religious fervor with her fellow nuns until 1226, when she died from tuberculosis. The news of Beatrice's sainthood quickly spread all over the district and many generous offers and gifts were given to the nunnery. In 1576 the nuns of the convent of Gemola were moved to Padua and the remains of Santa Beatrice were brought the church of Santa Sofia.
In 1657, after a period in which the nunnery lied in a state of neglect, it appears to be the property of a Venetian merchant. The transformation of the convent into a villa dates to this period; the “barchessa” was only added in the early 21st century, greatly spoiling the area of the old cemetery. The accurate survey realized before the building refurbishment promoted by public authorities in 1970s and 1980s revealed important traces of the ancient convent.
Today, some rooms on the ground floor host the naturalistic collection of the province museum where aspects of vegetation and fauna of Euganean Hills and the surrounding area are well illustrated.