The Stiftsbäckerei has been grinding its own rye flour since 2010, using electricity from its own water wheel. For this Franz Grabmer designed a combination of 3 millstones including sieve machines. In contrast to grinding in one single operation, this prevents the grist from heating up, which means that valuable ingredients are retained. The grinding products are conveyed pneumatically in a hygienic manner. A part of the mill, the largest millstone (pictured), can be seen in the vestibule of the bakery.

The rye is sourced from an organic farmer in the Waldviertel (Forest Quarter, Lower Austria). Consistent quality is given by storing a year's supply in the Stifts- und Salzachmühle. Before delivery to the Stiftsbäckerei, any weed seeds that may be present are sorted out optically using a state-of-the-art machine (Sortex).