There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them, but also on the comparative performance methodological approaches for their study. We used and compared two viral sequences enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA) for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining Operational Taxonomic Units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is advised because it consistently provided a more comprehensive description of the analysed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.