Mg/Ca ratios in planktonic foraminifera reflect calcification temperatures and are thus useful for sea surface temperature (SST) reconstructions. Despite the obvious utility of this paleoceanographic tracer, problems of dissolution, gametogenic calcification, and contaminant phases have thus far limited confidence in Mg/Ca-based reconstructions. Here we show strong evidence of Mg heterogeneity in foraminiferal calcite by sequentially measuring the composition of different forms of calcite (ontogenetic, gametogenic, diagenetic) in the same shells, while monitoring and removing contaminant phases. A new flow-through method combines chromatographic technology and inductively coupled plasma mass spectrometry (ICP-MS) in a series of cleaning and dissolution reactions monitored continuously with time-resolved analysis (TRA). This combination of slow, controlled dissolution and TRA provides a complete elemental description of contaminant phases and sorts the cleaned calcium carbonate based on dissolution sensitivity. Examination of partially dissolved shells with electron microscopy suggests that the flow-through method simulates the natural dissolution sequence and effectively separates the different calcite domains within a single foraminiferal shell. Heterogeneity of Mg/Ca in foraminiferal calcite is clearly demonstrated in flow-through analysis. Foraminiferal shells have initially high Mg levels that decrease steadily throughout dissolution. Later dissolution yields lower Mg/Ca, which is likely due to a combination of subsurface calcification and biomineralization effects. Mg/Ca ratios from the most dissolution-sensitive (high-Mg) portions of surface-dwelling species in core tops are used to calculate calcification temperatures. A comparison of late Holocene core top data with World Ocean Atlas SST data indicates that the flow-through method does yield viable SST estimates. Furthermore, a depth transect in the eastern tropical Pacific suggests that this approach provides the opportunity to extract initial calcification temperatures despite partial dissolution of foraminiferal shells.