<h3>Abstract</h3> <i>Cassava common mosaic virus</i> (CsCMV) is a potexvirus that causes systemic infections in cassava plants, leading to chlorotic mosaic and producing significant yield losses. To date, the physiological alterations and the mechanism underlying biotic stress during the cassava-CsCMV compatible interaction remains unknown. In this study, we found that CsCMV infection adversely modified chloroplast structure and had functional effects on chloroplasts in source leaves during the course of viral infection. Extrusion of the chloroplast membrane with amoeboid-shaped appearance was observed in infected mesophyll cells. These alterations were associated with lower relative chlorophyll content, and reduced PSII efficiency and CO<sub>2</sub> fixation. Moreover, an oxidative stress process was observed in CsCMV-infected plants. Strong declines in the maximum quantum yield of primary photochemistry (F<sub>v</sub>/F<sub>m</sub>) were observed in infected plants. Furthermore, the analysis of Chlorophyll-a fluorescence (ChlF) evidenced a progressive loss of both oxygen evolving complex activity and “connectivity” within the tripartite system (core antenna-LHCII-Reaction Centre). Other effects of the pathogen included reduction of starch and maltose content in source leaves, and a significant increase of the sucrose/starch ratio, which indicates alteration pattern of carbon. Our results suggest that CsCMV induces chloroplast distortion associated with progressive chloroplast function loss and diversion of carbon flux in source leaf tissue, which should be key in inducing yield losses of infected crops. <h3>Main conclusion</h3> CsCMV infection adversely modified chloroplast structure and had functional effects on chloroplasts during the course of viral infection, associated with metabolic adjustment in cassava source leaves, which would partly explain cassava root yield losses.