This study demonstrates that significant matrix‐dependent bias occurs during the measurement of Li mass fractions by SIMS in silicate glasses. This bias is particularly evident for basaltic and ultramafic samples, where published SIMS data of reference materials show discrepancies up to 40% compared with other measurement techniques. Matrix effects can be successfully corrected by taking into account the SiO2 content of the analysed material. New matrix‐corrected SIMS data for a suite of silicate glass reference materials are presented (glasses from MPI‐DING, USGS, Smithsonian and NIST, with a range of 46–76 g per 100 g SiO2), which are on average within 4% of preferred values (PV) as published in the GeoReM database. As several PV for Li in GeoReM are biased by the inclusion of inaccurate SIMS data, updated reference values are proposed that include the new SIMS dataset presented here.