Historical building techniques have been pointed out as a sample of local resistance to colonial technical influence during the early modern period, although this could not be proven by chemical analysis. A clay brick with an attached lime mortar sample was acquired from the former San Francisco Church’s foundation in Intramuros, Manila, Philippines and representative portions (BRK-1, BRK-2, BRK-3, MTR-1, MTR-2, and MTR-3) of the sample were utilized for chemical analysis using various analytical techniques. These are the energy dispersive x-ray fluorescence (EDXRF), Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM) and ultraviolet-visible spectroscopy (UV-Vis) for quantifying organic compounds. The clay brick sample is made of typical sand and clay specifically composed of non-calcareous clay and low refractory fluxes. The brick’s firing temperature was determined to be between 600°C to 800°C in an oxidizing environment. The attached lime mortar sample is probably manufactured using crushed seashells and classified as a hydraulic lime where clayey and sand particles serving as pozzolans. The lime mortar’s microstructure shows that it is well carbonated. Possible organic compounds specifically egg whites (albumen) which may have been added to the lime mortar yielded negative results. Both qualitative tests (Xanthoproteic Test, Ninhydrin Test and Biuret Test) and quantitative assays (Biuret Assay and Bradford Assay) were not able to detect the presence of any proteinaceous compounds in the sample. It has been established based on this material sample that eighteenth century Asian builders working in Manila kept local traditions and rejected European preferences.