The energetic costs to generate calcium carbonate skeletons and shells in marine organisms remain largely speculative due to the scarcity of empirical data. However, this information is critical to estimate energetic limitations of marine calcifiers that can explain their sensitivities to changes in sea water carbonate chemistry in past, present and future marine systems. The cost of calcification was evaluated using larval stages of the purple sea urchin, Strongylocentrotus purpuratus. We developed a skeleton re-mineralization assay, in which the skeleton was dissolved in live larvae followed by a re-mineralization over a few days. During skeleton re-mineralization, energetic costs were estimated through the measurement of key metabolic parameters including whole animal metabolic rates, citrate synthase (CS) enzyme activities and mRNA expression as well as mitochondrial densities in the calcifying primary mesenchyme cells (PMCs). Minor increases in a CS activity and a 10-15% increase in mitochondrial densities in PMCs were observed in re-mineralizing larvae as compared to control larvae. Re-mineralization under three different pH conditions (pH 8.1, pH 7.6 and pH 7.1) decreased with decreasing pH accompanied by pronounced increases in CS expression levels and increased mitochondrial densities in PMCs at pH 7.6. Despite a prominent increase in mitochondrial density of primary mesenchyme cells, particularly in the calcifying cohort of this cell type, this work demonstrated a low overall metabolic response to increased mineralization rates on the whole animal level under both, high and low pH conditions. We conclude that calcification in sea urchin larvae is compromised under low pH conditions, associated with low energetic efforts to fuel compensatory processes.