The very low B/Ca ratios characteristic of some natural biogenic carbonates, are of interest for research in ocean acidification but represent an analytical challenge. We describe a method using a novel instrument configuration (ICP-QQQ), for which we are not aware of any previously published geological applications, and for coccoliths, a sample type unique in its low B content and organic phases. Detection limits as low as 0.41 mmol/mol were achieved. Isobaric interferences, out of the reach even for SF-ICP-MS, can be solved using this instrument, which permits the safe measurement of the lowest abundance Ca isotope ( 46 Ca). This allows maximizing the B concentration measured (matrix concentration up to 800 ppm Ca) while maintaining both B and Ca signals in counting mode. More significantly for low B samples, the ICP-QQQ is also able to overcome the interference of the ubiquitous 12 C tail on the 11 B mass, which otherwise leads to significant overestimates at very low B concentrations. This could be a reason for the significantly lower B/Ca ratios observed for the low B content interlaboratory calibration standards (Carrara and OKA), while matching for the high B content standards was good. Finally, results obtained in the analysis of coccoliths grown in laboratory culture seems to corroborate that SIMS analysis of the samples mounted in Indium leads also to B/Ca overestimates due to porosity effects, as previously observed using LA-ICP-MS. This approach also permits the interference-free measurement of P/Ca and S/Ca ratios, which could be used as indicators of the complete removal of the organic matter from the samples.