In 965 AD, Archbishop Bruno I of Cologne, youngest brother of Emperor Otto the Great, died. Bruno bequeathed in his will 100 pounds of silver and other gifts to the Church of St. Mary "for the completion of the monastery and cloisters." This referred to a Benedictine convent that was added to the church at an unknown date.
The Church of St. Maria im Kapitol as we know it today was built by Abbess Ida (d.1060), granddaughter of Otto II and Theophanu (who is buried at St. Pantaleon). The new building used the western wall and foundations of Bruno's church and had its choir over the Roman temple. It had a gallery in the west end, adopting the imperial design of the Palatine Chapel in Aachen.