Knowledge on the interaction between non-vascular plants and pathogens is very scarce. This study is the first to report on the transmission of a satellite-associated cucumber mosaic virus (CMVsat) into the moss Physcomitrium patens, and only the second report on the successful mechanical inoculation of a virus into P. patens. Inoculation was successful on agar and on soil, the latter possibly constituting a more natural environment for the interaction. Additionally, this growth condition allowed the monitoring of the infection for an extended period of time without contamination. The concentration of the CMVsat coat protein was higher in plants incubated for 10 days than those incubated for 5 days. The CMVsat infection did not activate the biosynthesis of salicylic acid in moss. Flavonoids were predominantly located near the outer part of the P. patens cell and in the nucleus, the major compound was quercetin and its concentration was higher after infection. Moreover, the concentration of indole-3-acetic acid (IAA) also increased. The level of CMVsat was lower in GH3-double knockouts which, under control conditions, showed higher IAA levels than wild type, and IAA did not change after infection in GH3-double knockouts. The high IAA concentrations in the knockouts could have been a factor that reduced viral infection. An interaction between SA, quercetin and IAA during the response of P. patens towards CMVsat is possible and therefore a challenging subject for future research. Graphical abstract: [Figure not available: see fulltext.]