Two late Miocene Tridacna (giant clam) shells from East Kalimantan (Indonesia) were investigated in order to evaluate their potential as subannually resolved paleoenvironmental archives. Via a combination of X-ray diffraction (XRD), laser ablation–inductively coupled plasma–mass spectrometry (LA-ICPMS) trace element analysis, scanning electron microscopy (SEM) and cathodoluminescence (CL) imaging, pristine versus diagenetically altered domains within the shells were identified. LA-ICPMS transects targeting altered aragonite and calcite zones reveal distinct compositional differences in elemental ratios (B/Ca, Mg/Ca, Sr/Ca/ Ba/Ca, Mn/Ca, Al/Ca, La/Ca, Ce/Ca) relative to primary shell aragonite. Pristine shell domains are characterized by an intact banding pattern of alternating dark and light growth bands, with which spatially resolved LA-ICPMS element/Ca and micromilled δ18O records were aligned. Light δ18O values correspond to dark growth bands, indicating growth during warm seasons. The Mg/Ca and/or Sr/Ca ratios covary with oscillating stable oxygen isotope profiles. Progressive increase in Mg/Ca with age demonstrates that besides temperature, growth kinetics exert control over Mg incorporation. If interpreted as temperature controlled only, δ18O from both shells represents average seasonal sea-surface temperature (SST) variability of 2.7 ± 2.1 and 4.6 ± 1.7 °C, respectively. Using published temperature equations and assuming δ18Osw = −0.88‰, corresponding mean annual paleo–sea-surface temperatures of 27.8 ± 0.2 and 28.5 ± 0.2 °C are estimated. Although the fossil Tridacna shells were noticeably affected by alteration on their external surfaces, their internal aragonitic structure is, to a large extent, well preserved. These corresponding paleoproxy records provide detailed insight into tropical SST variability of the Indo-Pacific region during the late Miocene.