The biomass of aquatic organisms largely determines the mass and energy flow within an ecosystem, but the long-term impact of environmental change on biomass is not well constrained for a number of clades. Here, we test the hypothesis that bivalve biomass is negatively impacted by warming climate over time. This study is based on a fossil marine bivalve fauna recovered from hemipelagic sediments deposited in the eastern Mediterranean during climate cycles (marine isotope stages (MIS) 22-18; 900-712 kyr B.P.) of the Early-Middle Pleistocene Transition. We reconstruct individual shell biomasses from fossils and discuss the various biotic and abiotic factors that controlled long-term shell biomass patterns across this important interval in the Earth climate system. The results are contrary to the original hypothesis, suggesting that the response to temperature is not universal. Nevertheless, a decrease in median biomass is observed during the MIS 19 warm period and can be possibly attributed to the combined effect of multiple drivers that cooperated at that critical time in the past, including higher temperature and primary productivity, reduced ventilation of the sea floor, biodiversity changes due to geographic range shifts, and considering species- and age-specific thermal tolerances. Generally, bivalve biomass at the community level is determined by relative abundance and shell biomass-frequency distribution. In our study, the relative abundance and median biomass of small species do not increase or decrease, respectively, in warmer periods. However, larger species are negatively affected by warming both in terms of relative abundance and biomass.