The Church of the Company of Jesus in Quito (1605-1765) is one of the most remarkable examples of colonial religious architecture on the World Heritage List. This church has multiple constructive phases and several interventions with no clear record of the entire architectural site, including the historical mortars. A total of 14 samples of coating mortars inside the central nave were taken, with the protocols suggested by the research team and a comparative sample of the architectural group that does not have intervention. The analysis presented in this paper focuses on mineralogical characterization, semi-quantitative analysis by X-ray diffraction and scanning electron microscopy with microanalysis of the samples. The results showed the presence of volcanic aggregate lime and gypsum, used in lining mortars and joint mortars. Mineralogical and textural composition data have allowed the mortar samples to be relatively dated.