The late 16th or 17th century residence became home to the influential Sarsfield family and served as the manor house for the estate of Tully. While Lewis's Topographical Dictionary noted in 1837 that the house was then occupied by William Dunne, local historian Fitzgerald wrote in the early 1900s that "of Tully castle not one stone stands on another", suggesting the house built by Mr James Fay likely incorporated materials from the medieval castle. The original Tully House, shown on the 1838 Ordnance Survey map, was eventually demolished and replaced by the modern building that now stands within the Japanese Gardens at the Irish National Stud.

The site's medieval heritage runs deep. When Henry VIII dissolved the monasteries, an inquisition in 1540 revealed the preceptory's impressive holdings: a castle or fortilage, orchards, gardens, 60 acres of arable land, three houses, 100 additional acres, and a watermill, along with various rents and customs from tenants. Archaeological excavations in 1998 uncovered over one hundred glazed medieval potsherds, animal bones, and domestic refuse; likely secondary deposits used as infill for marshy ground but originally associated with the 13th century Knights Hospitallers commandery. The manor passed through various hands after the dissolution, with Queen Elizabeth I granting it to Sir William Sarsfield in 1569, before King Charles I formally created the Manor of Tully in 1628, complete with rights to hold two fairs and two weekly markets.

The site witnessed dramatic events during the Irish Confederate Wars. In February 1647, while Tully Preceptory served as a garrison for the Irish Confederate army under General Sarsfield, Parliamentarian forces under Colonel Jones arrived to negotiate surrender terms. During these talks, a fire broke out at a house near what was then described as Tully Castle or "Chief House". As soldiers rushed to help, fighting erupted at the gates, with Parliamentarian forces eventually seizing the nearby church. Today, while the original structures have vanished, the location remains significant as part of the Irish National Stud grounds, its layers of history preserved more in documents and archaeological finds than in standing stones.