The introduction of Next Generation Sequencing (NGS) techniques for forensic use has greatly expanded the possibilities of extracting information from biological stain materials in crime cases. However, the NGS workflows are not fully optimized for continuous, high-throughput processing of samples in forensic genetic laboratories. Although the Ion PGM™ has been on the market since 2010, the process of preparing samples for sequencing is still rather cumbersome and involves a large number of pipetting steps. This creates variability in the loading of the sequencing chips and in the sequencing coverage. This variability in turn complicates the interpretation of the results, i.e., low coverage leads to locus or allele dropout for poor performing markers. In order to automate a part of the sample preparation, we used the Ion Chef™ (Life Technologies) to prepare pooled Ion AmpliSeq™ libraries for emulsion PCR and loading onto sequencing chips. The workload and the number of manual pipetting steps were decreased while the chip loading efficiency, uniformity of loading and reproducibility was increased using the Ion Chef™ compared to the performance obtained with the more manual setup using the Ion OneTouch™ 2 system.