Complement recently identified as a “synaptic organizer” in the central nervous system (CNS). Specifically, it emerged that, beside dictating synapse remodelling during development and in neurodegenerative processes, complement also modulates glutamate release from cortical presynaptic terminals (synaptosomes) and astrocytic processes (gliosomes), controlling excitatory transmission and synaptic strength in this brain region. In both particles, the complement-evoked glutamate release relied on glutamate transporters (EAAT1 and 2) working in the reverse mode.We extended our study to synaptosomes and gliosomes from the cortex of mice suffering from experimental autoimmune encephalomyelitis (EAE) at the acute phase of the disease (21 d.p.i.). The results unveiled an increase of CD11b, GFAP and PSD95 density, but not SNAP25, in the cortex of EAE mice when compared to controls, suggestive of local inflammation and synaptic adaptations. Furthermore, C1q and C3 protein immunostainings increased in EAE cortical synaptosomes and gliosomes, despite the absence of evident signs of ongoing apoptosis or altered viability in these particles. Changes in complement density were paralleled by altered complement-evoked glutamate exocytosis, which is amplified in gliosomes and reduced in synaptosomes from EAE mice. The alteration of glutamate release was paralleled by an increased density of the EAAT1 protein in gliosomes (supporting the amplified complement-evoked glutamate exocytosis) and a reduced EAAT2 expression in synaptosomes (consistent with the reduced releasing activity of complement in these particles). In conclusion, we propose that complement organiser activity at glutamatergic cortical synapses is altered in EAE mice, potentially contributing to the onset of symptoms observed during multiple sclerosis.