Fired bricks were valued as essential building materials in the central tradition of Byzantine architecture in Constantinople (İstanbul), Anatolia, and the Balkans. In this study, Byzantine bricks from three construction periods, covering nearly nine centuries (fifth–fourteenth centuries), of Anaia Church (Kadıkalesi) in Western Anatolia were investigated to determine their characteristics, raw material properties, and production technologies. The characteristics of the bricks were evaluated and compared in order to identify similarities and differences between the periods and to investigate the continuity of the tradition of brick production over centuries. Basic physical and colorimetric properties, chemical and mineralogical compositions, thermal behavior, and microstructural and mechanical properties of bricks were determined by scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (SEM–EDS), Fourier-transform infrared spectrometry (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and mechanical tests. The results indicated that all the bricks in the Anaia Church were brown-beige colored, highly porous, low-density materials with low mechanical strength. They were produced from Ca-rich clays, probably obtained from two different sources used during all construction periods. The mineralogical composition and thermal properties revealed that the bricks from the first and second periods were fired at between 800 and 900°C and the bricks from the third period were fired at < 850°C. Greater calcium content and firing temperatures were found to reduce the total porosity and the number of small pores (< 10 μm) and increase the mechanical strength of the bricks. The results of the study revealed no significant differences in the production of bricks, including raw material sources and kiln conditions, for the different construction periods of the church.