The past decade has seen rapid growth in the development, testing and use of wocDNA COI metabarcoding. Much effort has been expended in the development of laboratory, sequencing and bioinformatic methodologies for wocDNA COI metabarcoding and for metabarcoding as a whole. However, while much progress has been made towards harmonisation of lab and sequencing methods, bioinformatic processes have remained a tangle of varying software, pipelines and theoretical approaches, often suffering from underreported detail. This diversity allows for versatility, especially for those who are well-informed and experienced in bioinformatics and able to pick and choose the appropriate approach. However, choosing from the range of approaches could easily hinder new applications of metabarcoding for researchers coming from a limited bioinformatic background, and high heterogeneity can stymie the potential for future reviews and meta-analyses. Our review, which is the first evaluating the state of the art on this topic, highlights that this danger is clearly present in the field of metazoan wocDNA COI metabarcoding. The results of our assessment and the recommendations derived from it may help to improve bioinformatic harmonisation and thus the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.