Abstract: In this study, parameters of an acid-catalyzed direct extraction methylation method used for the determination of low-level lipid residues in the ceramic artifacts were investigated and optimized as a result of chemometric modeling techniques that enable comprehensive statistical data to be obtained with fewer analyses in the optimization studies. For this purpose, 25 amorphous unglazed ceramic artifacts found during the 1996–2021 excavations at the Küllüoba Höyük archaeological site were subjected to lipid residue determination. The ceramic samples extracted by the proposed method were analyzed by gas chromatography-mass spectrometry, and the lipid residues present in them were determined. According to the obtained fatty acid composition results, it can be said that the lipid residues in the analyzed ceramics are of both animal and plant origin. The ceramic artifact with the highest lipid residue concentration was selected, and the parameters of the extraction method were examined using the chemometric models. According to the response surface methodology, the extraction time and temperature should be high as long as the experimental conditions and environment allow for the extraction of the lipid residues in the ceramic artifacts, and the silylation process has a limited positive effect on the yield, but the extraction with methanol can be achieved successfully when the silylation process is not performed.