Saponins of Chenopodium quinoa (quinoa) are triterpene glycosides synthesized primarily via the mevalonate pathway. Cultivars with high saponin content are bitter and must be processed to render seeds of the pseudograin palatable. There is no information on the modulation of terpenoid biosynthesis in quinoa in response to pathogens. The objective of this study was to determine if Cucumber mosaic virus (CMV) infection impacts regulation of saponin biosynthesis in quinoa. Seven-week-old seedlings of cultivars with different saponin content in seeds (sweet ‘Jesse’, medium ‘QQ74’ and bitter ‘Red Head’) were mock inoculated or inoculated with CMV. Leaves were harvested at 1 or 4 days post inoculation (dpi) and used for RNASeq library preparation. Raw data were trimmed and mapped to quinoa reference genome. Differentially expressed genes were identified by DESeq2 and RT-qPCR. At 1 dpi, triterpene saponin biosynthesis activating regulator 1 (TSARL1) was increased in all cultivars, but at 4 dpi, both TSARL1 regulation and virus symptoms in the high saponin cultivar differed from those with lower saponin. In ‘Red Head’, CMV infection was systemic and TSARL1 gene was downregulated at 4 dpi, whereas in the lower saponin cultivars, ‘Jesse’ and ‘QQ74’, there was a local lesion response and the TSARL1 gene was upregulated. The role of saponin in tolerance to CMV is uncertain, and more research is needed to ascertain relationships among these compounds and virus infection.