An automated ion-exchange chromatography method is developed for the separation of copper (Cu) from biological samples prior to stable, naturally occurring, isotope analysis. The technique does not require Cu to be fully oxidized/reduced into either Cu+ or Cu2+. Distribution coefficients of Cu and other cations to the Cu-specific anion exchange resin enable the effective purification and separation of Cu from complex matrixes using a single, reusable chromatographic column, with the potential to be modified for varying sample types. The automated chromatography system (prepFAST-MC™) can process up to 60 samples per run at a rate of 36 samples per day on a single ion exchange column. Low carryover (<1%) combined with high yields (97 ± 3%) for multiple extractions is observed. Isotopic analyses of the Cu fraction by multi collector-inductively coupled plasma-mass spectrometry, produced accurate Cu stable isotope data (ERM-AE633). The repeatability was assessed to be better than 0.02‰ for pure standard solutions and biological samples, making this method suitable for future applications, such as medical research, that require high throughput for precise isotopic analysis.