Seasonal variations in fluxes of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) and the estimated temperatures based on TEX86 were examined in sinking particles collected using moored sediment traps in the eastern Atlantic upwelling regions. In the equatorial Guinea Basin, GDGT fluxes show a correlation with opal fluxes, implying that GDGTs are mainly transported via aggregation with diatoms. The flux-weighted TEX86H temperatures derived from particles collected both at 853 m and 3921 m depth correspond to the water temperature (24.1 °C) of ca. 50 m depth, where nitrate concentration starts to increase. This suggests that nutrient concentrations may affect the depth habitat of Thaumarchaeota, thereby influencing the TEX86-derived water temperatures. In the coastal upwelling off Namibia, TEX86H temperatures are similar to satellite-derived sea surface temperature (SST) during the warm season, but the record derived from the trap is delayed relative to the SST by approximately 26 days. Warm biases, however, occur during the cold season. Higher TEX86 values have been found within the oxygen minimum zones (OMZs) in the water column of coastal upwelling regions. Thus, contributions from GDGTs produced in OMZs might explain the warmer temperature estimates during the cold season in regions where OMZs are pronounced. This scenario could explain the observed warm bias off Namibia. We, therefore, suggest that in the eastern Atlantic upwelling systems, nutrient depth distribution and GDGTs produced in OMZs can be potential environmental factors influencing TEX86 in sinking particles. In paleoenvironmental records of TEX86, non-thermal signals have to be considered on regional scales.