Chenopodium quinoa plants inoculated with carnation mottle virus developed chlorotic local lesions restricted to the inoculated leaf when grown in a growth chamber under 25°C day/18°C night. In contrast, when plants were grown in a greenhouse under more extreme conditions (35–40°C day/10–15°C night), they were systemically infected and developed chlorotic lesions in upper non-inoculated leaves. Viral RNA and movement protein accumulation levels in the inoculated leaves and the size of the chlorotic lesions were similar, under local and systemic infection conditions, suggesting that neither viral replication nor cell to cell movement account for this differential behaviour. Immunohistochemical and in situ hybridization studies on minor and major veins and surrounding tissues of inoculated leaves revealed no significant differences in the pattern of invasion of phloem and non-phloem cells between local and systemically infected plants. Microscopical analyses indicated that the extent of infection in petioles of plants that did not develop systemic infection was restricted to one or two phloem bundles and did not spread to neighbouring tissues or other plant organs. Taken together, these results indicate that environmental factors influence systemic accumulation of virus after the phloem entry point in the long distance movement pathway of carnation mottle virus in C. quinoa plants. The influence of these environmental factors on the phloem transport of photoassimilates and on the systemic invasion of the virus is discussed.