Chelex 100 serves as a highly effective stationary phase for the separation of metal ions from proteins. A three-zone Chelex carousel process with four columns was developed previously for the removal of Zn ions from protein in a buffer solution. In this study, alternative Chelex carousel processes with different zone configurations and zone numbers were developed to improve one or more of the economic factors in the previous three-zone Chelex carousel process. To increase the throughput per bed volume, the regeneration and the re-equilibration zone can be combined into one zone. To reduce the product dilution and increase the throughput per bed volume, the length of the loading zone can be increased or the washing step can be moved out of the loading zone into a separate zone. Comparison of the alternative carousel processes showed that a two-zone carousel with three columns in the loading zone is the most economical for zinc removal from protein.