This study investigated, at the microscopic level, whether the differential defence responses of soybean cultivars that are resistant (Fundacep 59) and susceptible (TMG 132) to target spot, caused by Corynespora cassiicola, could be associated with an increase in the production of phenolics, flavonoids and lignin at the infection sites. Many larger necrotic lesions with yellow halos were noticed on the leaves of plants from cultivar TMG 132, in contrast to the leaves of plants from cultivar Fundacep 59. Necrotic lesions also developed on the petioles of leaves of plants from cultivar TMG 132, while on the petioles and veins of leaves of plants from cultivar Fundacep 59, the lesions were of purple colour. The growth of fungal hyphae was reduced on the leaves of plants from cultivar Fundacep 59, and an apparently high density of trichomes was found in comparison with the leaves of plants from cultivar TMG 132. An appressorium‐like structure was produced at one or both extremities of the conidium of C. cassiicola, preferentially at the major and minor veins on the adaxial leaf surface of plants from both cultivars. Most cells on the leaves of plants from cultivar Fundacep 59 reacted against C. cassiicola infection by accumulating phenolic‐like compounds, which contributed to the death of many fungal hyphae and a greater maintenance of cell integrity. In contrast, fungal hyphae grew without any impedance in the leaf cells of plants from cultivar TMG 132, which was associated with signs of intense leaf tissue disorganization. Stronger autofluorescence and deposition of lignin and flavonoids were found in the cells of leaves of plants from cultivar Fundacep 59, in contrast to cultivar TMG 132. It can be concluded that soybean resistance to target spot is probably dependent on the activation of the phenylpropanoid pathway.