The church interior conserves its original 16th century main altar, with four stories tall, contains indigenous, Italian, Flemish and Spanish influence and is covered in 24karat gold leaf. It contains a relief of San Bernardino surrounded by two groups of indigenous sculptures, who are helping to build the church. Above San Bernardino, there is a depiction of the Virgin of the Assumption and the Virgin of Xochimilco. The paintings represent episodes from the life of Jesus and have been attributed to Simon Pereyns and Andrés de la Concha. This is one of the few 16th-century altarpieces to have survived and the only one similar to it in size and construction is located in the monastery in Huejotzingo, Puebla.