The Ermelo church was not built with a single project. In fact, the architectural complex that we have today is the result of several building phases which took place over the centuries. The research and archaeological excavations carried out by Sandra Silva Nogueira brought up a hypothesis that suggests three building phases.
The first building phase of the Ermelo church corresponds to the monastery foundation in the twelfth century. According to the information provided by researchers, the apse, the side chapels, the naves, and the main frontage were built during this phase.
The second phase, which should have happened in the eighteenth century, corresponds to a difficult period of the Ermelo Monastery. The works performed during this period correspond to the reduction of three churches to a single nave, the lowering of the roof, the demolition of the South side chapel and the building of the rectory, the bell tower, and the sacristy.
The third phase includes the works carried out in the church during the twentieth century, which brought improvements and a better functionality to the temple. The building of the clock tower and the fencing of the access to the high choir correspond exactly to this timeframe. This tower was demolished in the course of the works of appreciation on the surroundings of the church. The rubble was removed from the outer and inner walls, the roof was repaired, and three exterior doors were rebuilt. It was also in this time that the nave's ceiling paintings were scraped and five medallions of figurative elements were eliminated.