This study investigates the possibility of storing virus yellows RNA samples at –20°C and determining the most suitable sample type for such storage, between plant sap and total RNA. We quantified the RNA content of three types of virus yellows and the host plant by measuring Cq values using RT-qPCR. The experiments were carried out on two different scales and settings: a smaller experiment with 20 single-infection samples, and a larger experiment with 80 random mixed-infection samples to represent lab-controlled and practical field data, respectively. We compared the statistical significance of differences in measurement data before and after 6 months of storage at –20°C. Our results revealed that RNA of virus yellows from sugar beet remains detectable in comparable quantities after –20°C storage as in the initial total RNA, regardless of the sample type used. This observation aligns with our hypothesis that RNA from both sample types of virus yellows displays higher stability than previously established and can be preserved at –20°C for long-term storage. These findings underscore the possibility of using –20°C freezing system as an alternative to –80°C, which is commonly adopted as the standard in molecular laboratories to prevent RNA degradation. Our data can enable more informed research planning involving virus yellows RNA by providing greater flexibility in storage costs and space.