In this study, the mineralogical composition of 284 sherds obtained from the sites of Yeşilova Höyük and Yassıtepe Höyük, two of the oldest settlements in Western Anatolia, and corresponding to a wide period starting from the Neolithic period to the Chalcolithic and Early Bronze Age (EBA), was studied by attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. FTIR data was used to classify the sherds and state their firing conditions as a result of determining their mineralogical composition using principal component analysis (PCA), multivariate curve resolution (MCR), and hierarchical cluster analysis (HCA). According to the PCA results, the second-order derivative FTIR spectrum with 19 smoothing points in the range of 1300–400 cm−1 was determined to be the most successful model in classifying sherds. As a result of MCR, which allows comparison of standard minerals obtained within the scope of the study, it was determined that kaolinite, illite, chlorite, and some feldspar types were dominant in the sherds. According to HCA analysis, all sherds except five of them exhibited a similar mineralogical structure. According to the derivative spectra, it was seen that the sherds had a composition consisting of kaolinite, illite, hematite, chlorite, and some feldspar types at different rates. Upon examining the data, it becomes evident that the sherds are composed of nearly identical minerals and might have been fired in an oxidizing atmosphere. Even while 279 sherds had many mineralogical traits, N-061, EB-030, N-043, C-068, and N-059 were found to have distinct proportions of comparable minerals, including more kaolinite, illite, calcite, and chlorite. Regarding color, additives, and the amount of ceramic pastes present, these five sherds differ from the others. This suggests that there might have been attempts at manufacture or pots brought in from outside the Yeşilova Höyük-Yassıtepe Höyük sites. The results provided from the derivative spectra showed that all sherds except five of them have been fired at about at temperatures slightly above 450–500 °C due to their relatively low kaolinite character, but below 800 °C because diopside and similar high-temperature minerals could not be detected. The five sherds may have been fired at a temperature of around 450–500 °C due to the presence of a high character of kaolinite, illite, and chlorite. It was understood that the residents of the sites of Yeşilova Höyük and Yassıtepe Höyük produced their ceramics using the same raw materials and the same production methods from the Neolithic period to EBA thanks to FTIR and chemometrics, which are very good tools for analyzing large numbers of sherds with low cost and fast analysis time.