1563 Queen Elizabeth I commissioned Thomas Wood a former soldier and civil servant, to survey and value the estate. In 1570 Thomas Wood started to rebuild the Hall, but he died in 1584 and it remained incomplete until 1710. During this time  5th Baronet decided to complete the work with York architect William Etty commissioned to oversee it. Most of the present building of Kilnwick Percy Hall was the work of John Carr from York who designed a grand hall to be built in front of the Elizabeth Hall. The work was finally completed in 1800.

Kilnwick Percy Hall was requisitioned for military use during World War II. Officially is was used for the sorting of Forces Mail and a “special  mission” training centre. Soon after two thirds of the hall was demolished for economic reasons. This made the hall economically viable to become a large family home which it remained for a long time until  purchased by Madhyamaka Centre.

Initially giving teachings in Hebden Bridge, then soon moving to York, in 1981 the Centre moved into  a suite of offices and in 1983 it purchased a Georgian town-house in the centre of York. This became the first residential centre to be established by Geshe Kelsang. By 1986 the Centre had outgrown the house and began to look for larger premises.