The monastery is situated in an area already inhabited during the Great Moravian period. Benedictine abbey in Hronský Beňadik was first mentioned in 1075. Historical significance of the monument accentuates also the vastness of its properties donated to the monastery by Hungarian king Gejza and listed in the founding charter. The extent of the properties has greatly changed in later years.

The monastery was built in a strategic location, so called Slovak gate. It laid on the crossroad of important trade routes joining Nitra region with the mining cities via the Hron river valley. It had a traditional four-wing ground plan with cloister around the paradise garden and the church situated on the north side.

King Gejza entrusted the abbey to the Order of St. Benedict. Benedictines, skilled in crafts as well as in agriculture, became the pioneers both in spiritual and cultural sphere. The Abbey in Hronský Beňadik also possessed rich deposits of the precious metals found in the region. Among the monks there were specialists in metallurgy, mining, technical or religious buildings. Many of these examples of the architecture have been preserved for example in Banská Štiavnica to this day.

Due to frequent property disputes, pope Innocent III confirmed estates to the abbey in 1209. The significance of the monastery in the region then rose again. In the pope's charter, the small village below the monastery is also already mentioned.

In the 14th century, the Benedictine abbey in Hronský Beňadik fell into decay. The new church was allegedly built in times of the abbot Siegfried and his successors, after the year 1330. The construction, however, stretched for a long time and the current church of St. Benedict the Abbot and the Virgin Mary was consecrated only in 1483.

The arrival of the Turks to the vicinity of Hronský Beňadik in the 16th century also directly threatened nearby mining cities. The monastery therefore turned into a renaissance fortress and the church was also converted into a multi-storey bastion in the years 1565 – 1588. Barracks, warehouses, gunpowder mill, guardhouse and other bastions were added to the object. The monastery functioned as a fort until the middle of the 18th century.

In the meantime, even the last Benedictines left one by one and the abbey in Hronský Beňadik eventually came under the administration of the Chapter of Esztergom in 1565.

Considerably damaged monastery buildings underwent a vast reconstruction again in the year 1752. The town of Hronský Beňadik gained the market rights in 1680 and the grain market became particularly popular. The west wing of the former Benedictine monastery was consequently converted into a granary.

Another extensive reconstruction, led by the Sopron architect Franz Storno and his sons Koloman and Franz, began in the year 1882. They aimed to regotizate the monument based on the then valid preservation methods. Foundations of the original Romanesque three nave basilica from the 11th century were discovered during the restoration works in the church of St. Benedict the Abbot and the Virgin Mary. The basilica did not have a north nave nor an apse as in today’s church; however it was positioned within the cloister. Back in the 11th century the basilica served only the needs of the monks, as the territory of Hronský Beňadik was not inhabited at that time.

In the 20th century, the monastery was administrated by the Order of Salesians of Don Bosco. The Divine Redeemer Sisters were interned in Hronský Beňadik in 1951. Then the Salesians returned to the monastery again and lived there until the year 1999, when the Pallotines took over.