An inkjet printer has process color printheads and spot color printheads each comprising a plurality of inkjet nozzles. The printheads are arranged such that the spot color printhead has fewer nozzles allocated for each spot color then the process color printhead has allocated for each process color. For areas requiring spot color printing the printing rate may be reduced or the dot size and/or the dot spacing may be varied for spot colors to enable printing at the same rate as for process colors.