At the expense of Don Diego de Tapia, son of Don Fernando (Conín), founder of the city of Queretaro, the convent was built in 1606 to give shelter to the religious vocation of his daughter Maria Luisa of the Holy Spirit.

In the colonial era, the Temple of Santa Clara was one of the most important and wealthiest of New Spain.

Currently all that remains is the preserved temple and a small annex because during the Reform War much of the construction was destroyed.