The structure of a bioinformatic metabarcoding pipeline will depend strongly on the research aim, amplification and sequencing protocols, target locus, and target biodiversity fraction. The diversity of bioinformatic tasks and the software approaches to implement them is of course beneficial for designing appropriate pipelines, but such heterogeneity may also restrict integrated, standardised and synergistic growth in the field. As metazoan wocDNA metabarcoding becomes more accessible to researchers from a range of fields and backgrounds, harmonisation of bioinformatic approaches is important to ensure (i) high-quality, reproducible data amenable to qualitative or  quantitative reviews and meta-analysis across studies, and (ii) a reliable, consistent methodology for wider implementation, development and expansion of wocDNA metabarcoding. We consider harmonisation not to mean strict prescription of the tasks and software to use, nor their order. Instead a harmonised field would recognise the diversity of approaches available, while recording key steps and establishing the effects of parameter choice on the outcome of metabarcoding studies. This approach could be enabled by the adoption of universal aligned standards for data generation and processing, while allowing for flexibility in implementation to adapt to varying research goals and take advantage of novel methodological development.