The increasing availability of new genome assemblies often comes with a paucity of associated genomic annotations, limiting the range of studies that can be performed. A common workaround is to lift over annotations from better annotated genomes. However, generating the files required to perform a liftover is computationally and labour intensive and only a limited number are currently publicly available. Here we present nf-LO (nextflow-LiftOver), a containerised and scalable Nextflow pipeline that enables liftovers within and between any species for which assemblies are available. nf-LO will consequently facilitates data interpretation across a broad range of genomic studies.