The terms acute and persistent have been used to describe symptomatic and asymptomatic host reactions to plant viruses respectively. Endornaviruses of pepper (Capsicum annuum) and melon (Cucumis melo) are persistent viruses that have been detected in many commercial bell pepper and melon cultivars. Therefore, when eating the fruits of these two plant species, we consume endornaviruses. We conducted experiments on the in-vitro effect of two common digestive enzymes and pH on the structural integrity of the viral dsRNA of bell pepper endornavirus (BPEV) and Cucumis melo endornavirus (CmEV), evaluated by gel electrophoresis and reverse-transcription polymerase chain reaction (RT-PCR). The effect of the amylase, pepsin, and pH treatments on the dsRNA of both viruses was similar. Amylase did not appear to affect the structural integrity of the viral dsRNAs. In contrast, gel electrophoresis analysis of pepsin-treated dsRNA samples showed an abnormal electrophoretic migration and evidence of partial dsRNA degradation. DsRNAs were partially degraded when exposed to a pH value of 2.0 and completely degraded at a pH value of 1.0. Our results suggest that under the simulated gastric conditions used in this investigation, the structural integrity of the dsRNA of BPEV and CmEV can be negatively affected. Nevertheless, it is likely that our lower digestive organs are exposed to both, fragmented and full viral replicative intermediate dsRNA of these two endornaviruses.