Although the contract of 1767 was restricted to the facade of the church, it is likely that Gonzales was soon contracted to finish the rest of the church. He undoubtedly finished the sacristy and made it the temporary church about 1770. By 1772, the ribs to support the vaulting had been built above the pilasters except in the area of the choir loft. Later evidence, in the drawings of Edward Everett in 1847 and on the wall of the church itself, indicates that the choir loft had been built. The ribs at the crossing of the transept, one of those that would support the dome, were also in place and the vaulting had been completed over the sanctuary.
In spite of his oath, Gonzales did not complete the church of Valero. In 1772 the Querétaran Franciscans left and all the missions were placed in Zacatecan hands. At that point, the priority shifted from the completion of Valero to the completion of the church at San José; Gonzales was probably transferred to work full-time on this project.
He had completed the foundation of San José church in early 1768, and began work on the above-grade construction of the walls after the ceremony dedicating the cornerstone on March 19. Soon afterwards, when the walls were perhaps two feet above grade, Gonzales changed Losoya’s original design. This was a cost-cutting redesign that shortened the building by 37 feet, removed the transepts, and created the sacristy and its splendid window in the same baroque style as the facade of the church.
About 1770, Gonzales may have enlarged the San José granary and converted it to a temporary church with the addition of a choir loft and stairs, and painted decorations on the interior, traces which can still be seen in the building. At the same time flying buttresses were constructed on the exterior of the building to help support the vaulted roof.
At Espada, about 1770, construction began on a new wood-vaulted granary designed and built by Gonzales, apparently located just east of the old granary. This was later converted to the permanent church of Espada, only to collapse or burn out within a year or two.
The granaries of San Juan and Espada were Gonzales’s last projects. He was apparently an old man when he started work on Valero in the mid-1760s, and by the mid-1770s seems to have been showing his age. The missionaries hired a younger architect to help or replace him about 1773. Dionicio Gonzales and his wife continued to live in San Fernando until their deaths in 1789.