San Miguel mill in Oñati was once part of the stately complex of San Miguel monastery, over which its secular lords, the Counts of Oñati, had the exclusive tithe right.

The Counts owned at least three mills in the valley throughout the 15th century: Olalde (sold to another powerful local family, the Lazarragas), Linazibar and San Miguel, the latter two were documented for the first time in 1440 and 1432 respectively.

In 1983, the Council of Oñati acquired the old San Miguel mill from the nuns of the convent of Santa Ana but, in 1997, it was demolished in order to build a block of flats, where the archaeological remains of the flour production were preserved on the ground floor.

The San Miguel mill museum still houses some of the original elements, but has also incorporated pieces from other mills and, to complete the site, has had some new pieces copied from models from other sources. Today it is possible to visit the museum as it is located inside the tourist office.