The geochemical composition of foraminifera shells from an Ocean Drilling Program site in the Panama Basin has been analyzed by several analytical techniques (LA-ICP-MS, ICP-MS, XRD, SEM, EDX) in order to identify and evaluate the occurrence of contaminant phases which may bias paleoenvironmental reconstructions. LA-ICP-MS results on uncleaned tests indicate the presence of Mn-Mg-rich contaminant phases at the inner surfaces of the foraminiferal shells (which have Mn/Ca ratios up to 400 mmol mol−1 and Mg/Ca ratios up to 50 mmol mol−1). We have rigorously assessed the ability of different cleaning protocols to remove these contaminant phases and have obtained satisfactory results only when a reductive step is included. The analysis of cleaning residuals collected after each of the different cleaning steps applied reveals that high Mn values are associated with at least two different contaminant phases, of which only one is linked to high Mg values. XRD analysis further reveals that the Mn-Mg-rich phase is the Ca-Mn-Mg carbonate kutnahorite (Ca(Mn, Mg)(CO3)2). Our results demonstrate that the presence of kutnahorite-like minerals can bias Mg/Ca ratios toward higher values (by 7–36%) and lead to significant overestimation of past seawater temperatures (by 0.9 up to 6.2°C, in the case of these Panama Basin samples).