This three-aisled Romanesque basilica was built by German colonists in the early 13th century. It was probably remodeled in Gothic style in the early 15th century, when a new presbytery and Chapel of the Virgin Mary were added. In the mid-15th century, troops of Ján Jiskra of Brandýs fortified it with four corner bastions. The church burned in 1676 and was extensively rebuilt in 1699–1711. The main altar and others were consecrated in 1715 by Lukáš Natali, Bishop of Belgrade. After several more fires, the last major reconstruction took place in 1925–1926: the apse closing the north aisle and the crypts beneath the altars were demolished, the main altar was restored, and painter Elemér Dedinský created a monumental painting above the triumphal arch.
Krupina sa začala formovať po príchode nemeckých kolonistov v 13. storočí. Stredoveké mesto sa sústredilo okolo románskeho nemeckého kostola Narodenia Panny Márie a postupne sa vyvinulo hlavné námestie a predmestie. Na hlavnom, dnes Svätotrojičnom námestí, sa sústreďovali domy najbohatších krupinských mešťanov, neskôr i radnica a konávali sa tu týždenné trhy a výročné jarmoky. Na predmestí (Malý rínok a priľahlé ulice) sa sústredili domy slovenských obyvateľov mesta.