A down-core comparison of two commonly applied foraminiferal cleaning procedures for Mg/Ca paleothermometry has been conducted using well-preserved Globigerinoides ruber white (250–300 μm) from core material deposited under varying terrigenous-input and bottom water conditions. This study demonstrates that in the majority of investigated core materials, both cleaning methods yield fairly comparable results of Mg/Ca ratios. However, Fe and Mn phases are effectively removed by the cleaning procedure containing a reductive step. In a core interval indicating gradual transition of terrigenous deposition and pore water conditions, the cleaning procedure without a reductive step results in anomalously higher Mg/Ca ratios accompanied by high Fe/Ca and Mn/Ca ratios, indicating the presence of high-Mg contaminants. Considering that the Mg/Ca deviation of the comparison study is the cumulative sum of (1) the difference in cleaning efficiency of the applied methods, (2) the cleaning-method-dependent partial dissolution of Mg, and (3) the heterogeneity of subsamples, we suggest that selective Mg loss from well-preserved Globigerinoides ruber shells caused by the reductive sample treatment is not substantial enough to significantly bias paleotemperature estimation. Thus, for core material deposited under varying sources and amounts of terrigenous material and bottom water conditions favorable for formation of authigenic mineral phases, the use of cleaning methods that do include a reductive step yields more effective cleaning results by successful removal of mineral phases that may contain high Mg.