nf-core/eager is an efficient, portable, and accessible pipeline for processing and screening ancient (meta)genomic data. This re-implementation of EAGER into Nextflow and nf-core will improve reproducibility and scalability of rapidly increasing aDNA datasets, for both large and small laboratories. Extensive documentation also enables newcomers to the field to get a practical understanding on how to interpret aDNA in the context of NGS data processing. Ultimately, nf-core/eager provides easier access to the latest tools and routine screening analyses commonly used in the field, and sets up the pipeline for remaining at the forefront of palaeogenetic analysis.