We report an investigation of the mechanisms involved in the formation of nanostructured epoxy thermosetting systems using highly epoxidized poly(styrene-b-isoprene-b-styrene) (eSIS) block copolymer at three different stages of the curing process. In the uncured state, polystyrene (PS) blocks self-assembled in sphere-like nanodomains with a short-range order, while epoxidized polyisoprene (ePI) subchains were initially miscible with the epoxy precursors. As the curing reaction proceeded, the PS nanodomains became gradually distorted switching to bigger and less organized structures. This effect is due to reaction-induced microphase separation of ePI subchains which became immiscible with the epoxy system as the curing process occurs. However, this demixing process was partial because of the reaction between ePI subchains and the epoxy matrix, which reduced ePI subchains mobility. Non expulsed ePI fraction increased the epoxy matrix mean glass transition temperature (T-g) in (20-25) degrees C. Moreover, it was demonstrated that the epoxidation degree of ePI subchains affected the final obtained nanostructured pattern of the thermosetting materials, switching from distorted and interconnected sphere-like nanodomains when the epoxidation degree is 65% to sphere-like nanostructures for 100% of epoxidation.