Background. Actinobacillus pleuropneumoniae (APP) and Streptococcus suis are major bacterial pathogens of swine, where rapid and accurate serotype identification is essential for surveillance, outbreak investigations and vaccine selection. Current serotyping methods are labour-intensive, often rely on multiple molecular assays or specialised reagents, and are not readily deployable within routine diagnostic laboratories. Methods. We developed and validated an end-to-end Oxford Nanopore Technologies (ONT) workflow encompassing bacterial culture, optimisation of DNA extraction and library preparation, whole-genome sequencing and automated serotype prediction. Multiple laboratory workflows, including different DNA extraction methods and direct-from-colony sequencing were evaluated to identify protocols suitable for routine diagnostics and a novel bioinformatics pipeline was developed for automated serotype assignment using species-specific capsular polysaccharide loci and validated using reference genomes, publicly available genomes and field isolates. Results. Optimised laboratory workflows consistently generated high-quality sequencing data suitable for genome reconstruction and serotype prediction. The pipeline was evaluated using >100 publicly available genomes, and 12 field isolates, achieving 98% concordance with expected serotypes while successfully distinguishing closely related capsule types. Comparison of laboratory workflows identified practical protocols that reduced hands-on processing and the complete workflow enabled automated serotype prediction within <24 hours from bacterial colony and has been successfully transferred for validation within diagnostic laboratories. Conclusion. This study demonstrates a complete culture-to-serotype ONT workflow integrating laboratory optimisation with an automated Nextflow-based serotyping pipeline for two important veterinary pathogens. The approach provides a practical framework for rapid, reproducible whole-genome-based serotyping and supports wider implementation of ONT sequencing within veterinary diagnostic laboratories.