Whole-organism community DNA (wocDNA) metabarcoding has become a necessary and powerful tool to study mixed communities from bulk samples by detecting short DNA sequences. This review integrates the use of arthropods as ecological indicators through wocDNA metabarcoding, covering key methodological aspects from sampling design to bioinformatics, and highlighting ASV-based (Amplicon Sequence Variants) pipelines for incorporating haplotype-level variation. The success of wocDNA metabarcoding relies on proper sampling methods, good laboratory practices, cleaning of bulk samples, selecting suitable arthropod sizes, efficient DNA extractions, accurate library quantification, appropriate genetic markers for accurate taxonomic identification, and effective sequence filtering. Incorporating haplotype data into monitoring unveils intraspecific variation that could complement species-level diversity, thus enhancing conventional analyses. Choosing abundance- or incidence-based approaches is key for selecting appropriate statistical methods. WocDNA metabarcoding provides biodiversity estimates for entire communities and allows researchers to derive insights that can inform the formulation or refinement of hypotheses. These refined hypotheses, based on the obtained biodiversity estimates, can then guide ecosystem conservation.