Signaling in host plants is an integral part of a successful infection by pathogenic RNA viruses. Therefore, identifying early signaling events in host plants that play an important role in establishing the infection process will help our understanding of the disease process. In this context, phosphorylation constitutes one of the most important post-translational protein modifications, regulating many cellular processes. In this study, we aimed to identify the processes affected by peanut stunt virus (PSV) and its satellite RNA (satRNA) infection in Nicotiana benthamiana at the early stage of pathogenesis. To achieve this, we performed proteome and phosphoproteome analyses on plants treated with PSV and its satRNA. The analysis of the number of differentially phosphorylated proteins showed strong down-regulation in phosphorylation in virus-treated plants (without satRNA). Moreover, the proteome analysis revealed more down-regulated proteins in PSV+satRNA-treated plants, which indicated a complex dependence between proteins and their modifications. Apart from changes in photosynthesis and carbon metabolism usually observed in virus-infected plants, alterations in proteins involved in RNA synthesis, transport, and turnover were observed. This is the first community resource on the proteome and phosphoproteome of cucumovirus and its satRNA infection in N. benthamiana constituting a valuable data set for future studies.