jats:pWe present a new procedure for the separation and purification of Cu and Zn from geological samples. Our procedure employed a single pass, triple‐stack column set‐up. The first column, filled with TRU resin (TrisKem International), quantitatively removed Fe and Ti from sample matrices. A second column, filled with pre‐filter resin (TrisKem International), removed organic compounds. Finally, a third column, filled with anion exchange resin (AG1‐X8, 200–400 mesh, Bio‐Rad), was used to separate Cu and Zn from the remaining matrix. Our procedure required about 50% less acid volume than previously reported methods for Cu and Zn separation, thereby minimising analytical blanks and column running times. Copper and Zn stable isotope ratios were determined by a Thermo Neptune Plus MC‐ICP‐MS using Zn and Cu external normalisation, respectively, in addition to sample‐standard bracketing to correct for instrumental mass bias. We explore the inter‐calibration of Cu and Zn isotope fractionation coefficients during analysis by measuring mixed Cu–Zn solutions with enhanced mass bias variation generated by varying sample gas flow rates. Our results demonstrate that this procedure is useful when variation in instrumental mass bias throughout analytical sequences is insufficient to inter‐calibrate Cu and Zn fractionation coefficients.</jats:p>