Differential accumulation of the distinct genome segments is a common feature of viruses with segmented genomes. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". There is speculation and some experimental support for a functional role of the genome formula by modulating gene expression through copy number variations. However, the mechanisms of genome formula regulation have not yet been identified. In this study, we investigated whether the genome formula of the octopartite nanovirus faba bean necrotic stunt virus (FBNSV) is regulated by processes acting at the individual segment vs. viral population levels. We used a leaf infiltration system to show that the two most accumulated genome segments of the FBNSV possess a greater intrinsic accumulation capacity in Vicia faba tissues than the other segments. Nevertheless, processes acting at the individual segment level are insufficient to generate the genome formula, suggesting the involvement of additional mechanisms acting at the supra-segment level. Indeed, the absence of segments with important functions during systemic infection strongly modifies the relative frequency of the others, indicating that the genome formula is a property of the segment group. Together, these results demonstrate that the FBNSV genome formula is shaped by a complex process acting at both the individual segment and the segment group levels. Segmented and multipartite viruses have their genomic information carried by several molecules, which allows for the unequal accumulation of the different genome segments in infected tissues. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". The genome formula is host-dependent and believed to modulate gene expression through copy number variations upon host switches. The mechanisms leading to the genome formula remain unknown. Here, we determined that the genome formula of an octopartite single-stranded DNA nanovirus is shaped by processes acting both at the level of individual segments, some having higher accumulation rates, and at the level of the group of segments, the omission of some non-essential segments affecting the relative accumulation of others. Our study provides insights into the level at which genome formula regulation operates, giving a starting point for future studies aiming at elucidating the mechanisms governing genome formula in multipartite and segmented viruses.