Individuals with eating disorders (EDs) often engage in exercise no matter potential negative long-term outcomes (e.g., weight loss, injury). Yet exercising may temporarily attenuate ED symptoms, but whether exercise also affects network structure and pairwise associations of ED symptoms remained unclear. We used a novel approach called Moderated Multilevel Graphical Vector Autoregression to estimate changes in psychopathology networks from before to after exercising in ecological momentary assessment data from 102 individuals with EDs across multiple days (M = 22.14, SD = 5.40; range: 6–22 days) at 4 times daily. Between-person and within-person temporal networks were computed, obtaining stable centrality coefficients for temporal networks only. In those, autoregressive effects of several symptoms, including binge-eating, overeating, or weighing oneself, were attenuated when participants previously exercised. Exercise mostly downregulated temporal effects of ED symptoms on other symptoms, including effects of binge eating and other compensatory behaviors on feeling guilty after the most recent meal, vomiting on weighing oneself, and overeating on fear of weight gain. Our study highlights the complex dynamic effects of exercise on ED symptoms in daily life and calls for novel studies investigating mechanisms of exercise to inform treatments targeting detrimental long-term effects of exercise in EDs.