The geological collections have also always been present in the Royal Seminary of Bergara, especially from the mineralogical works of the Royal Seminary Patriotic Bascongado at the time of the Enlightenment, but also throughout the next century.

Recall that for the needs of the pioneering studies of mineralogy and metallurgy, initiated in 1777, the Seminary had a rich mineralogical cabinet which in the organization and enrichment among others intervened Ramón María de Munibe and Fausto Elhuyar. The mineralogical collection lasted throughout the XIX century, being enriched with the entry of new materials, as happened in 1872 when the old seminarist, eminent engineer and geologist and President of the Commission for the Geological Map of Spain, Mr. D. Felipe Bauza donated to the Institute a rich array of minerals owned. 369 fossils and 1181 minerals are inventoried.