There are clear differences in genome architecture over organisms, however its evolution is poorly understood. Here, we study three specific processes of the evolution of genome architecture in viruses: (i) the reshuffling of existing elements, (ii) the decrease of genome complexity through loss of redundant or unnecessary genetic material, and (iii) the increase of genome complexity through the acquisition of new genes. We address these topics in vivo using a plant RNA virus as a model organism. Important changes in the viral genome were generated followed by experimental evolution to observe how these changes were accommodated. The evolved and ancestral lineages were compared by next-generation sequencing and measurements of virulence, viral accumulation and within-host competitive fitness. First, we identified multiple barriers to the evolution of alternative gene orders. Second, we observed differences in the deletion dynamics of genetically and functionally redundant sequences and we developed a model to predict the stability of gene insertions. Third, we found an exogenous sequence that was evolutionary stable in our model virus genome that does not appear to affect viral fitness and can act as a backup in case of failure of the viral protein responsible for blocking RNAi-mediated plant defenses. Lastly, we observed that a host species jump can be a game changer for evolutionary dynamics, allowing unstable viruses to be competitive in alternative hosts. The results of this study serve as a road map for future research on genome architecture evolution across different viruses as well as different organisms.