Correlating metal to calcium (Me/Ca) ratios of marine biogenic carbonates, such as bivalve shells, to environmental parameters has led to contradictory results. Biogenic carbonates represent complex composites of organic and inorganic phases. Some elements are incorporated preferentially into organic phases, and others are incorporated into inorganic phases. Chemical sample pretreatment to remove the organic matrix prior to trace element analysis may increase the applicability of the investigated proxy relationship, though its efficiency and side effects remain questionable. We treated inorganic calcium carbonate and bivalve shell powder (Arctica islandica) with eight different chemical treatments including H2O2, NaOH, NaOCl, and acetone and analyzed the effects on (1) Me/Ca ratios (Sr/Ca, Mg/Ca, Ba/Ca, and Mn/Ca), (2) organic matter (≈N) content, and (3) mineralogical composition of the calcium carbonate. The different treatments (1) cause element and treatment specific changes of Me/Ca ratios, (2) vary in their efficiency to remove organic matter, and (3) can even alter the phase composition of the calcium carbonate (e.g., formation of Ca(OH)2 during NaOH treatment). Among all examined treatments there were none without any side effects. In addition, certain Me/Ca changes we observed upon chemical treatment contradict our expectations that lattice-bound elements (Sr and Ba) should not be affected, whereas non-lattice-bound elements (Mg and Mn) should decrease upon removal of the organic matrix. For instance, we observe that NaOCl treatment did not alter Sr/Ca ratios but caused unexpected changes of the Mg/Ca ratios. The latter demonstrates that the buildup of complex biogenic composites like the shell of Arctica islandica are still poorly understood. Copyright 2011 by the American Geophysical Union.